Characterization of nitrifying microbial community in a submerged membrane bioreactor at short solids retention times.

PubMed

Duan, Liang; Song, Yonghui; Xia, Siqing; Hermanowicz, Slawomir W

2013-12-01

This study investigated the nitrifying bacterial community in membrane bioreactor (MBR) at short solids retention times (SRTs) of 3, 5 and 10 days. The denaturing gradient gel electrophoresis results showed that different types of ammonia-oxidizing bacteria (AOB) can survive at different operating conditions. The diversity of AOB increased as the SRT increased. The real-time PCR results showed that the amoA gene concentrations were similar when MBRs were stabilized, and it can be a good indicator of stabilized nitrification. The results of clone library indicated that Nitrosomonas was the dominant group of AOB in three reactors. The microarray results showed that Nitrospira was the dominant group of nitrite-oxidizing bacteria (NOB) in the system. All groups of AOB and NOB except Nitrosolobus and Nitrococcus were found in MBR, indicated that the nitrifying bacterial community structure was more complicated. The combination of some molecular tools can provide more information of microbial communities. Copyright © 2013 Elsevier Ltd. All rights reserved.

Interactions of Nitrifying Bacteria and Heterotrophs: Identification of a Micavibrio-Like Putative Predator of Nitrospira spp.

PubMed Central

Dolinšek, Jan; Lagkouvardos, Ilias; Wanek, Wolfgang; Wagner, Michael

2013-01-01

Chemolithoautotrophic nitrifying bacteria release soluble organic compounds, which can be substrates for heterotrophic microorganisms. The identities of these heterotrophs and the specificities of their interactions with nitrifiers are largely unknown. In this study, we incubated nitrifying activated sludge with 13C-labeled bicarbonate and used stable isotope probing of 16S rRNA to monitor the flow of carbon from uncultured nitrifiers to heterotrophs. To facilitate the identification of heterotrophs, the abundant 16S rRNA molecules from nitrifiers were depleted by catalytic oligonucleotides containing locked nucleic acids (LNAzymes), which specifically cut the 16S rRNA of defined target organisms. Among the 13C-labeled heterotrophs were organisms remotely related to Micavibrio, a microbial predator of Gram-negative bacteria. Fluorescence in situ hybridization revealed a close spatial association of these organisms with microcolonies of nitrite-oxidizing sublineage I Nitrospira in sludge flocs. The high specificity of this interaction was confirmed by confocal microscopy and a novel image analysis method to quantify the localization patterns of biofilm microorganisms in three-dimensional (3-D) space. Other isotope-labeled bacteria, which were affiliated with Thermomonas, colocalized less frequently with nitrifiers and thus were commensals or saprophytes rather than specific symbionts or predators. These results suggest that Nitrospira spp. are subject to bacterial predation, which may influence the abundance and diversity of these nitrite oxidizers and the stability of nitrification in engineered and natural ecosystems. In silico screening of published next-generation sequencing data sets revealed a broad environmental distribution of the uncultured Micavibrio-like lineage. PMID:23335755

Bacterial aggregation and biofilm formation in a vortical flow

PubMed Central

Yazdi, Shahrzad; Ardekani, Arezoo M.

2012-01-01

Bacterial aggregation and patchiness play an important role in a variety of ecological processes such as competition, adaptation, epidemics, and succession. Here, we demonstrate that hydrodynamics of their environment can lead to their aggregation. This is specially important since microbial habitats are rarely at rest (e.g., ocean, blood stream, flow in porous media, and flow through membrane filtration processes). In order to study the dynamics of bacterial collection in a vortical flow, we utilize a microfluidic system to mimic some of the important microbial conditions at ecologically relevant spatiotemporal scales. We experimentally demonstrate the formation of “ring”-shaped bacterial collection patterns and subsequently the formation of biofilm streamers in a microfluidic system. Acoustic streaming of a microbubble is used to generate a vortical flow in a microchannel. Due to bacteria's finite-size, the microorganisms are directed to closed streamlines and trapped in the vortical flow. The collection of bacteria in the vortices occurs in a matter of seconds, and unexpectedly, triggers the formation of biofilm streamers within minutes. Swimming bacteria have a competitive advantage to respond to their environmental conditions. In order to investigate the role of bacterial motility on the rate of collection, two strains of Escherichia coli bacteria with different motilities are used. We show that the bacterial collection in a vortical flow is strongly pronounced for high motile bacteria. PMID:24339847

Investigation of Archaeal and Bacterial community structure of five different small drinking water networks with special regard to the nitrifying microorganisms.

PubMed

Nagymáté, Zsuzsanna; Homonnay, Zalán G; Márialigeti, Károly

2016-01-01

Total microbial community structure, and particularly nitrifying communities inhabiting five different small drinking water networks characterized with different water physical and chemical parameters was investigated, using cultivation-based methods and sequence aided Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis. Ammonium ion, originated from well water, was only partially oxidized via nitrite to nitrate in the drinking water distribution systems. Nitrification occurred at low ammonium ion concentration (27-46μM), relatively high pH (7.6-8.2) and over a wide range of dissolved oxygen concentrations (0.4-9.0mgL(-1)). The nitrifying communities of the distribution systems were characterized by variable most probable numbers (2×10(2)-7.1×10(4) MPN L(-1)) and probably originated from the non-treated well water. The sequence aided T-RFLP method revealed that ammonia-oxidizing microorganisms and nitrite-oxidizing Bacteria (Nitrosomonas oligotropha, Nitrosopumilus maritimus, and Nitrospira moscoviensis, 'Candidatus Nitrospira defluvii') were present in different ratios in the total microbial communities of the distinct parts of the water network systems. The nitrate generated by nitrification was partly utilized by nitrate-reducing (and denitrifying) Bacteria, present in low MPN and characterized by sequence aided T-RFLP as Comamonas sp. and Pseudomonas spp. Different environmental factors, like pH, chemical oxygen demand, calculated total inorganic nitrogen content (moreover nitrite and nitrate concentration), temperature had important effect on the total bacterial and archaeal community distribution. Copyright © 2016 Elsevier GmbH. All rights reserved.

Urea Amendment Decreases Microbial Diversity and Selects for Specific Nitrifying Strains in Eight Contrasting Agricultural Soils

PubMed Central

Staley, Christopher; Breuillin-Sessoms, Florence; Wang, Ping; Kaiser, Thomas; Venterea, Rodney T.; Sadowsky, Michael J.

2018-01-01

Application of nitrogen (N) fertilizers, predominantly as urea, is a major source of reactive N in the environment, with wide ranging effects including increased greenhouse gas accumulation in the atmosphere and aquatic eutrophication. The soil microbial community is the principal driver of soil N cycling; thus, improved understanding of microbial community responses to urea addition has widespread implications. We used next-generation amplicon sequencing of the 16S rRNA gene to characterize bacterial and archaeal communities in eight contrasting agricultural soil types amended with 0, 100, or 500 μg N g-1 of urea and incubated for 21 days. We hypothesized that urea amendment would have common, direct effects on the abundance and diversity of members of the microbial community associated with nitrification, across all soils, and would further affect the broader heterotrophic community resulting in decreased diversity and variation in abundances of specific taxa. Significant (P < 0.001) differences in bacterial community diversity and composition were observed by site, but amendment with only the greatest urea concentration significantly decreased Shannon indices. Expansion in the abundances of members of the families Microbacteriaceae, Chitinophagaceae, Comamonadaceae, Xanthomonadaceae, and Nitrosomonadaceae were also consistently observed among all soils (linear discriminant analysis score ≥ 3.0). Analysis of nitrifier genera revealed diverse, soil-specific distributions of oligotypes (strains), but few were correlated with nitrification gene abundances that were reported in a previous study. Our results suggest that the majority of the bacterial and archaeal community are likely unassociated with N cycling, but are significantly negatively impacted by urea application. Furthermore, these results reveal that amendment with high concentrations of urea may reduce nitrifier diversity, favoring specific strains, specifically those within the nitrifying genera

Understanding Nitrifier Denitrification: How far are we?

NASA Astrophysics Data System (ADS)

Wrage-Mönnig, N.

2014-12-01

Nitrifier denitrification is the oxidation of ammonia (NH3) via hydroxylamine (NH2OH) to nitrite (NO2-) and subsequent reduction of NO2- via nitric oxide (NO) to the greenhouse gas nitrous oxide (N2O) and possibly to dinitrogen (N2) by autotrophic nitrifiers. Especially in recent years, a lot of research has been conducted on this pathway. Under some conditions, it might dominate the N2O production from soils. Methods for studying nitrifier denitrification include selective inhibition, stable isotope and isotopomer methods, molecular and modelling approaches. They are applied from pure culture and pot studies to the field scale, trying to improve our knowledge of the conditions and factors controlling nitrifier denitrification. But how far are we? What have we learned so far and what remains to be discovered? With this contribution, I am trying to give an update of our understanding of this less well-known but important pathway.

Bacterial and iron oxide aggregates mediate secondary iron mineral formation: green rust versus magnetite.

PubMed

Zegeye, A; Mustin, C; Jorand, F

2010-06-01

In the presence of methanoate as electron donor, Shewanella putrefaciens, a Gram-negative, facultative anaerobe, is able to transform lepidocrocite (gamma-FeOOH) to secondary Fe (II-III) minerals such as carbonated green rust (GR1) and magnetite. When bacterial cells were added to a gamma-FeOOH suspension, aggregates were produced consisting of both bacteria and gamma-FeOOH particles. Recently, we showed that the production of secondary minerals (GR1 vs. magnetite) was dependent on bacterial cell density and not only on iron reduction rates. Thus, gamma-FeOOH and S. putrefaciens aggregation pattern was suggested as the main mechanism driving mineralization. In this study, lepidocrocite bioreduction experiments, in the presence of anthraquinone disulfonate, were conducted by varying the [cell]/[lepidocrocite] ratio in order to determine whether different types of aggregate are formed, which may facilitate precipitation of GR1 as opposed to magnetite. Confocal laser scanning microscopy was used to analyze the relative cell surface area and lepidocrocite concentration within the aggregates and captured images were characterized by statistical methods for spatial data (i.e. variograms). These results suggest that the [cell]/[lepidocrocite] ratio influenced both the aggregate structure and the nature of the secondary iron mineral formed. Subsequently, a [cell]/[lepidocrocite] ratio above 1 x 10(7) cells mmol(-1) leads to densely packed aggregates and to the formation of GR1. Below this ratio, looser aggregates are formed and magnetite was systematically produced. The data presented in this study bring us closer to a more comprehensive understanding of the parameters governing the formation of minerals in dense bacterial suspensions and suggest that screening mineral-bacteria aggregate structure is critical to understanding (bio)mineralization pathways.

Bacterial nitrification in chloraminated water supplies.

PubMed Central

Cunliffe, D A

1991-01-01

Nitrifying bacteria were detected in 64% of samples collected from five chloraminated water supplies in South Australia and in 20.7% of samples that contained more than 5.0 mg of monochloramine per liter. Laboratory experiments confirmed that nitrifying bacteria are relatively resistant to the disinfectant. Increased numbers of the bacteria were associated with accelerated decays of monochloramine within distribution systems. The combination of increased concentrations of oxidized nitrogen with decreased total chlorine residuals can be used as a rapid indicator of bacterial nitrification. PMID:1781698

Monochloramine Cometabolism by Nitrifying Biofilm Relevant ...

EPA Pesticide Factsheets

Recently, biological monochloramine removal (i.e., cometabolism) by a pure culture ammonia–oxidizing bacteria, Nitrosomonas europaea, and a nitrifying mixed–culture have been shown to increase monochloramine demand. Although important, these previous suspended culture batch kinetic experiments were not representative of drinking water distribution systems where bacteria grow predominantly as biofilm attached to pipe walls or sediments and physiological differences may exist between suspension and biofilm growth. Therefore, the current research was an important next step in extending the previous results to investigate monochloramine cometabolism by biofilm grown in annular reactors under drinking water relevant conditions. Estimated monochloramine cometabolism kinetics were similar to those of ammonia metabolism, and monochloramine cometabolism was a significant loss mechanism (25–40% of the observed monochloramine loss). These results demonstrated that monochloramine cometabolism occurred in drinking water relevant nitrifying biofilm; thus, cometabolism may be a significant contribution to monochloramine loss during nitrification episodes in distribution systems. Investigate whether or not nitrifying biofilm can biologically transform monochloramine under drinking water relevant conditions.

Bacterial density and community structure associated with aggregate size fractions of soil-feeding termite mounds.

PubMed

Fall, S; Nazaret, S; Chotte, J L; Brauman, A

2004-08-01

The building and foraging activities of termites are known to modify soil characteristics such as the heterogeneity. In tropical savannas the impact of the activity of soil-feeding termites ( Cubitermes niokoloensis) has been shown to affect the properties of the soil at the aggregate level by creating new soil microenvironments (aggregate size fractions) [13]. These changes were investigated in greater depth by looking at the microbial density (AODC) and the genetic structure (automated rRNA intergenic spacer analysis: ARISA) of the communities in the different aggregate size fractions (i.e., coarse sand, fine sand, coarse silt, fine silt, and dispersible clays) separated from compartments (internal and external wall) of three Cubitermes niokoloensis mounds. The bacterial density of the mounds was significantly higher (1.5 to 3 times) than that of the surrounding soil. Within the aggregate size fractions, the termite building activity resulted in a significant increase in bacterial density within the coarser fractions (>20 mum). Multivariate analysis of the ARISA profiles revealed that the bacterial genetic structures of unfractionated soil and soil aggregate size fractions of the three mounds was noticeably different from the savanna soil used as a reference. Moreover, the microbial community associated with the different microenvironments in the three termite mounds revealed three distinct clusters formed by the aggregate size fractions of each mound. Except for the 2-20 mum fraction, these results suggest that the mound microbial genetic structure is more dependent upon microbial pool affiliation (the termite mound) than on the soil location (aggregate size fraction). The causes of the specificity of the microbial community structure of termite mound aggregate size fractions are discussed.

Culture-independent detection of 'TM7' bacteria in a streptomycin-resistant acidophilic nitrifying process

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kurogi, T.; Linh, N. T. T.; Kuroki, T.

2014-02-20

Nitrification in biological wastewater treatment processes has been believed for long time to take place under neutral conditions and is inhibited under acidic conditions. However, we previously constructed acidophilic nitrifying sequencing-batch reactors (ANSBRs) being capable of nitrification at < pH 4 and harboring bacteria of the candidate phylum 'TM7' as the major constituents of the microbial community. In light of the fact that the 16S rRNA of TM7 bacteria has a highly atypical base substitution possibly responsible for resistance to streptomycin at the ribosome level, this study was undertaken to construct streptomycin-resistant acidophilic nitrifying (SRAN) reactors and to demonstrate whethermore » TM7 bacteria are abundant in these reactors. The SRAN reactors were constructed by seeding with nitrifying sludge from an ANSBR and cultivating with ammonium-containing mineral medium (pH 4.0), to which streptomycin at a concentration of 10, 30 and 50 mg L{sup −1} was added. In all reactors, the pH varied between 2.7 and 4.0, and ammonium was completely converted to nitrate in every batch cycle. PCR-aided denaturing gradient gel electrophoresis (DGGE) targeting 16S rRNA genes revealed that some major clones assigned to TM7 bacteria and Gammaproteobacteria were constantly present during the overall period of operation. Fluorescence in situ hybridization (FISH) with specific oligonucleotide probes also showed that TM7 bacteria predominated in all SRAN reactors, accounting for 58% of the total bacterial population on average. Although the biological significance of the TM7 bacteria in the SRAN reactors are unknown, our results suggest that these bacteria are possibly streptomycin-resistant and play some important roles in the acidophilic nitrifying process.« less

Nitrifying moving bed biofilm reactor (MBBR) biofilm and biomass response to long term exposure to 1 °C.

PubMed

Hoang, V; Delatolla, R; Abujamel, T; Mottawea, W; Gadbois, A; Laflamme, E; Stintzi, A

2014-02-01

This study aims to investigate moving bed biofilm reactor (MBBR) nitrification rates, nitrifying biofilm morphology, biomass viability as well as bacterial community shifts during long-term exposure to 1 °C. Long-term exposure to 1 °C is the key operational condition for potential ammonia removal upgrade units to numerous northern region treatment systems. The average laboratory MBBR ammonia removal rate after long-term exposure to 1 °C was measured to be 18 ± 5.1% as compared to the average removal rate at 20 °C. Biofilm morphology and specifically the thickness along with biomass viability at various depths in the biofilm were investigated using variable pressure electron scanning microscope (VPSEM) imaging and confocal laser scanning microscope (CLSM) imaging in combination with viability live/dead staining. The biofilm thickness along with the number of viable cells showed significant increases after long-term exposure to 1 °C. Hence, this study observed nitrifying bacteria with higher activities at warm temperatures and a slightly greater quantity of nitrifying bacteria with lower activities at cold temperatures in nitrifying MBBR biofilms. Using DNA sequencing analysis, Nitrosomonas and Nitrosospira (ammonia oxidizers) as well as Nitrospira (nitrite oxidizer) were identified and no population shift was observed between 20 °C and after long-term exposure to 1 °C. Copyright © 2013 Elsevier Ltd. All rights reserved.

Bacteria of the Candidate Phylum TM7 are Prevalent in Acidophilic Nitrifying Sequencing-Batch Reactors

PubMed Central

Hanada, Akiko; Kurogi, Takashi; Giang, Nguyen Minh; Yamada, Takeshi; Kamimoto, Yuki; Kiso, Yoshiaki; Hiraishi, Akira

2014-01-01

Laboratory-scale acidophilic nitrifying sequencing-batch reactors (ANSBRs) were constructed by seeding with sewage-activated sludge and cultivating with ammonium-containing acidic mineral medium (pH 4.0) with or without a trace amount of yeast extract. In every batch cycle, the pH varied between 2.7 and 4.0, and ammonium was completely converted to nitrate. Attempts to detect nitrifying functional genes in the fully acclimated ANSBRs by PCR with previously designed primers mostly gave negative results. 16S rRNA gene-targeted PCR and a subsequent denaturating gradient gel electrophoresis analysis revealed that a marked change occurred in the bacterial community during the overall period of operation, in which members of the candidate phylum TM7 and the class Gammaproteobacteria became predominant at the fully acclimated stage. This result was fully supported by a 16S rRNA gene clone library analysis, as the major phylogenetic groups of clones detected (>5% of the total) were TM7 (33%), Gammaproteobacteria (37%), Actinobacteria (10%), and Alphaproteobacteria (8%). Fluorescence in situ hybridization with specific probes also demonstrated the prevalence of TM7 bacteria and Gammaproteobacteria. These results suggest that previously unknown nitrifying microorganisms may play a major role in ANSBRs; however, the ecophysiological significance of the TM7 bacteria predominating in this process remains unclear. PMID:25241805

Cyanate as energy source for nitrifiers

PubMed Central

Palatinszky, Marton; Herbold, Craig; Jehmlich, Nico; Pogoda, Mario; Han, Ping; von Bergen, Martin; Lagkouvardos, Ilias; Karst, Søren M.; Galushko, Alexander; Koch, Hanna; Berry, David; Daims, Holger; Wagner, Michael

2015-01-01

Ammonia- and nitrite-oxidizers are collectively responsible for the aerobic oxidation of ammonia via nitrite to nitrate and play essential roles for the global biogeochemical nitrogen cycle. The physiology of these nitrifying microbes has been intensively studied since the first experiments of Sergei Winogradsky more than a century ago. Urea and ammonia are the only recognized energy sources that promote the aerobic growth of ammonia-oxidizing bacteria and archaea. Here we report the aerobic growth of a pure culture of the ammonia-oxidizing thaumarchaeote Nitrososphaera gargensis1 on cyanate as the sole source of energy and reductant, the first organism known to do so. Cyanate, which is a potentially important source of reduced nitrogen in aquatic and terrestrial ecosystems2, is converted to ammonium and CO2 by this archaeon using a cyanase that is induced upon addition of this compound. Within the cyanase gene family, this cyanase is a member of a distinct clade that also contains cyanases of nitrite-oxidizing bacteria of the genus Nitrospira. We demonstrate by co-culture experiments that these nitrite-oxidizers supply ammonia-oxidizers lacking cyanase with ammonium from cyanate, which is fully nitrified by this consortium through reciprocal feeding. Screening of a comprehensive set of more than 3,000 publically available metagenomes from environmental samples revealed that cyanase-encoding genes clustering with the cyanases of these nitrifiers are widespread in the environment. Our results demonstrate an unexpected metabolic versatility of nitrifying microbes and suggest a previously unrecognized importance of cyanate for N-cycling in the environment. PMID:26222031

Population Ecology of Nitrifiers in a Stream Receiving Geothermal Inputs of Ammonium

PubMed Central

Cooper, A. Bryce

1983-01-01

The distribution, activity, and generic diversity of nitrifying bacteria in a stream receiving geothermal inputs of ammonium were studied. The high estimated rates of benthic nitrate flux (33 to 75 mg of N · m−2 · h−1) were a result of the activity of nitrifiers located in the sediment. Nitrifying potentials and ammonium oxidizer most probable numbers in the sediments were at least one order of magnitude higher than those in the waters. Nitrifiers in the oxygenated surface (0 to 2 cm) sediments were limited by suboptimal temperature, pH, and substrate level. Nitrifiers in deep (nonsurface) oxygenated sediments did not contribute significantly to the changes measured in the levels of inorganic nitrogen species in the overlying waters and presumably derived their ammonium supply from ammonification within the sediment. Ammonium-oxidizing isolates obtained by a most-probable number nonenrichment procedure were species of either Nitrosospira or Nitrosomonas, whereas all those obtained by an enrichment procedure (i.e., selective culture) were Nitrosomonas spp. The efficiency of the most-probable-number method for enumerating ammonium oxidizers was calculated to be between 0.05 and 2.0%, suggesting that measurements of nitrifying potentials provide a better estimate of nitrifying populations. PMID:16346261

Contrasting responses of bacterial and fungal communities to aggregate-size fractions and long-term fertilizations in soils of northeastern China.

PubMed

Liao, Hao; Zhang, Yuchen; Zuo, Qinyan; Du, Binbin; Chen, Wenli; Wei, Dan; Huang, Qiaoyun

2018-04-20

Soils, with non-uniform distribution of nutrients across different aggregate-size fractions, provide spatially heterogeneous microhabitats for microorganisms. However, very limited information is available on microbial distributions and their response to fertilizations across aggregate-size fractions in agricultural soils. Here, we examined the structures of bacterial and fungal communities across different aggregate-size fractions (2000-250 μm, 250-53 μm and <53 μm) in response to 35-years organic and/or chemical fertilization regimes in the soil of northeastern China by phospholipid fatty acid (PLFA) and high throughput sequencing (HTS) technology. Our results show that larger fractions (>53 μm), especially 250-53 μm aggregates, which contain more soil C and N, are associated with greater microbial biomass and higher fungi/bacteria ratio. We firstly reported the fungal community composition in different aggregate-size fractions by HTS technology and found more Ascomycota but less Zygomycota in larger fractions with higher C content across all fertilization regimes. Fertilization and aggregate-size fractions significantly affect the compositions of bacterial and fungal communities although their effects are different. The bacterial community is mainly driven by fertilization, especially chemical fertilizers, and is closely related to the shifts of soil P (phosphorus). The fungal community is preferentially impacted by different aggregate-size fractions and is more associated with the changes of soil C and N. The distinct responses of microbial communities suggest different mechanisms controlling the assembly of soil bacterial and fungal communities at aggregate scale. The investigations of both bacterial and fungal communities could provide a better understanding on nutrient cycling across aggregate-size fractions. Copyright © 2018. Published by Elsevier B.V.

Nitrification in histosols: a potential role for the heterotrophic nitrifier.

PubMed

Tate, R L

1977-04-01

Insufficient populations of Nitrosomonas and Nitrobacter were found in a Pahokee muck soil (Lithic medidaprit) to account for the nitrate concentration observed. To determine if heterotrophic nitrifiers could account for some of this discrepancy, a method was developed to measure the levels of heterotrophic nitrifiers in soil. A population of 4.1 X 10(5) Arthrobacter per g of dry fallow soil, capable of producing nitrite and/or nitrate from reduced nitrogenous compounds, was observed. Amendment of the much with 0.5% (wt/wt) sodium acetate and 0.1% (wt/wt) ammonium-nitrogen as ammonium sulfate (final concentrations) not only resulted in the usual increase in autotrophic nitrifiers, but also in a fourfold increase in the heterotrophic nitrifying Arrthrobacter. Amendment of like samples with N-Serve [2-chloro-6(trichloromethyl) pyridinel] prevented the increase in Nitrosomonas, but not that in the heterotrophic nitrifiers. Nitrate production in the presence of the inhibitor was diminished but not prevented. An Arthrobacter sp., isolated from the muck, produced nitrite when inoculated at high densities into sterile soil, unamended or amended with sodium acetate and/or ammomium sulfate. These data suggest that the heterotrophic population may be responsible for some of the nitrate produced in these Histosols.

Variation in heterotrophic and autotrophic nitrifier populations in relation to nitrification in organic soils.

PubMed

Tate, R L

1980-07-01

The occurrence of heterotrophic and autotrophic nitrifiers in Pahokee muck and the role of these organisms in the ecosystem were assessed by surveying their population densities under different field conditions and by observing the relationship of these populations with aerobic bacteria and soil moisture. Heterotrophic nitrifier populations varied from 2.0 x 10 to 3.8 x 10 bacteria per cm of muck in surface fallow (bare) Pahokee muck during the annual cycle. This population decreased 40-fold between the surface and the 60- to 70-cm depths of soil. Similar variations were noted with autotrophic nitrifier populations. Significant correlations were found between heterotrophic nitrifiers and both soil moisture and aerobic bacteria. These relationships did not exist for the autotrophic nitrifiers. In soil that had been heated to kill the autotrophic nitrifiers, while preserving a population of the heterotrophs, and then amended with sodium acetate or ammonium sulfate or both, no nitrate or nitrite accumulated, although significant increases in heterotrophic nitrifiers were detected. In unheated control soil, nitrate plus nitrite-N increased from 14.3 to 181 mug/g of wet soil, and 48 mug of nitrite-N per g was produced. These data suggest that the autotrophic nitrifiers were the sole population responsible for nitrification in Pahokee muck.

Effects of Ice-Algal Aggregate Export on the Connectivity of Bacterial Communities in the Central Arctic Ocean

PubMed Central

Rapp, Josephine Z.; Fernández-Méndez, Mar; Bienhold, Christina; Boetius, Antje

2018-01-01

In summer 2012, Arctic sea ice declined to a record minimum and, as a consequence of the melting, large amounts of aggregated ice-algae sank to the seafloor at more than 4,000 m depth. In this study, we assessed the composition, turnover and connectivity of bacterial and microbial eukaryotic communities across Arctic habitats from sea ice, algal aggregates and surface waters to the seafloor. Eukaryotic communities were dominated by diatoms, dinoflagellates and other alveolates in all samples, and showed highest richness and diversity in sea-ice habitats (∼400–500 OTUs). Flavobacteriia and Gammaproteobacteria were the predominant bacterial classes across all investigated Arctic habitats. Bacterial community richness and diversity peaked in deep-sea samples (∼1,700 OTUs). Algal aggregate-associated bacterial communities were mainly recruited from the sea-ice community, and were transported to the seafloor with the sinking ice algae. The algal deposits at the seafloor had a unique community structure, with some shared sequences with both the original sea-ice community (22% OTU overlap), as well as with the deep-sea sediment community (17% OTU overlap). We conclude that ice-algal aggregate export does not only affect carbon export from the surface to the seafloor, but may change microbial community composition in central Arctic habitats with potential effects for benthic ecosystem functioning in the future. PMID:29875749

Nitrifying bacterial biomass and nitrification activity evaluated by FISH and an automatic on-line instrument at full-scale Fusina (Venice, Italy) WWTP.

PubMed

Badoer, S; Miana, P; Della Sala, S; Marchiori, G; Tandoi, V; Di Pippo, F

2015-12-01

In this study, monthly variations in biomass of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) were analysed over a 1-year period by fluorescence in situ hybridization (FISH) at the full-scale Fusina WWTP. The nitrification capacity of the plant was also monitored using periodic respirometric batch tests and by an automated on-line titrimetric instrument (TITrimetric Automated ANalyser). The percentage of nitrifying bacteria in the plant was the highest in summer and was in the range of 10-15 % of the active biomass. The maximum nitrosation rate varied in the range 2.0-4.0 mg NH4 g(-1) VSS h(-1) (0.048-0.096 kg TKN kg(-1) VSS day(-1)): values obtained by laboratory measurements and the on-line instrument were similar and significantly correlated. The activity measurements provided a valuable tool for estimating the maximum total Kjeldahl nitrogen (TKN) loading possible at the plant and provided an early warning of whether the TKN was approaching its limiting value. The FISH analysis permitted determination of the nitrifying biomass present. The main operational parameter affecting both the population dynamics and the maximum nitrosation activity was mixed liquor volatile suspended solids (MLVSS) concentration and was negatively correlated with ammonia-oxidizing bacteria (AOB) (p = 0.029) and (NOB) (p = 0.01) abundances and positively correlated with maximum nitrosation rates (p = 0.035). Increases in concentrations led to decreases in nitrifying bacteria abundance, but their nitrosation activity was higher. These results demonstrate the importance of MLVSS concentration as key factor in the development and activity of nitrifying communities in wastewater treatment plants (WWTPs). Operational data on VSS and sludge volume index (SVI) values are also presented on 11-year basis observations.

Variation in Heterotrophic and Autotrophic Nitrifier Populations in Relation to Nitrification in Organic Soils †

PubMed Central

Tate, Robert L.

1980-01-01

The occurrence of heterotrophic and autotrophic nitrifiers in Pahokee muck and the role of these organisms in the ecosystem were assessed by surveying their population densities under different field conditions and by observing the relationship of these populations with aerobic bacteria and soil moisture. Heterotrophic nitrifier populations varied from 2.0 × 105 to 3.8 × 106 bacteria per cm3 of muck in surface fallow (bare) Pahokee muck during the annual cycle. This population decreased 40-fold between the surface and the 60- to 70-cm depths of soil. Similar variations were noted with autotrophic nitrifier populations. Significant correlations were found between heterotrophic nitrifiers and both soil moisture and aerobic bacteria. These relationships did not exist for the autotrophic nitrifiers. In soil that had been heated to kill the autotrophic nitrifiers, while preserving a population of the heterotrophs, and then amended with sodium acetate or ammonium sulfate or both, no nitrate or nitrite accumulated, although significant increases in heterotrophic nitrifiers were detected. In unheated control soil, nitrate plus nitrite-N increased from 14.3 to 181 μg/g of wet soil, and 48 μg of nitrite-N per g was produced. These data suggest that the autotrophic nitrifiers were the sole population responsible for nitrification in Pahokee muck. PMID:16345599

Population of Nitrifying Bacteria and Nitrification in Ammonium Saturated Clinoptilolite

NASA Technical Reports Server (NTRS)

McGilloway, R. L.; Weaver, R. W.; Ming, Douglas W.; Gruener, J.

1999-01-01

As humans begin to spend longer periods of time in space, plants will be incorporated into life support systems. Ammonium saturated clinoptilolite is one plant growth substrate but a balance between ammonium and nitrate is needed. A laboratory study was conducted to determine effects of nitrifying bacteria on ammonium concentrations and kinetics of nitrification. Columns containing clinoptilolite substrate amended with nitrifying bacteria obtained from soil enrichment were analyzed weekly for a 90 day period. The enrichment culture initially contained 1 x 10(exp 5) ammonium oxidizing bacteria and 1 x 10(exp 2) nitrite oxidizing bacteria per gram of substrate. Populations of ammonium oxidizing bacteria increased to 1 x 10(exp 6) and nitrite oxidizing bacteria increased to 1 x 10(exp 3) per gram of substrate. The nitrification rate was approximately 0.25mg NO3(-)-N/kg.hr. Experiments were also conducted to enumerate nitrifying bacteria in a clinoptilolite substrate used to grow wheat (Triticum aestivum L.). Seventy days following the initial inoculation with an unknown number of commercial nitrifying bacteria, 1 x 10(exp 5) ammonium oxidizing bacteria per gram of substrate were present. The number of nitrite oxidizing bacteria was between 1 x 10(exp 3) to 10(exp 4) per gram of substrate as measured by the most probable number method. Nitrification rates were approximately 0.20mg NO3(-)-N/kg.hr. Clinoptilolite readily exchanged sufficient concentrations of ammonium to support nitrifying bacteria and they survived well in this medium.

Quantitative response of nitrifying and denitrifying communities to environmental variables in a full-scale membrane bioreactor.

PubMed

Gómez-Silván, C; Vílchez-Vargas, R; Arévalo, J; Gómez, M A; González-López, J; Pieper, D H; Rodelas, B

2014-10-01

The abundance and transcription levels of specific gene markers of total bacteria, ammonia-oxidizing Betaproteobacteria, nitrite-oxidizing bacteria (Nitrospira-like) and denitrifiers (N2O-reducers) were analyzed using quantitative PCR (qPCR) and reverse-transcription qPCR during 9 months in a full-scale membrane bioreactor treating urban wastewater. A stable community of N-removal key players was developed; however, the abundance of active populations experienced sharper shifts, demonstrating their fast adaptation to changing conditions. Despite constituting a small percentage of the total bacterial community, the larger abundances of active populations of nitrifiers explained the high N-removal accomplished by the MBR. Multivariate analyses revealed that temperature, accumulation of volatile suspended solids in the sludge, BOD5, NH4(+) concentration and C/N ratio of the wastewater contributed significantly (23-38%) to explain changes in the abundance of nitrifiers and denitrifiers. However, each targeted group showed different responses to shifts in these parameters, evidencing the complexity of the balance among them for successful biological N-removal. Copyright © 2014 Elsevier Ltd. All rights reserved.

Nematode grazing promotes bacterial community dynamics in soil at the aggregate level

PubMed Central

Jiang, Yuji; Liu, Manqiang; Zhang, Jiabao; Chen, Yan; Chen, Xiaoyun; Chen, Lijun; Li, Huixin; Zhang, Xue-Xian; Sun, Bo

2017-01-01

Nematode predation has important roles in determining bacterial community composition and dynamics, but the extent of the effects remains largely rudimentary, particularly in natural environment settings. Here, we investigated the complex microbial–microfaunal interactions in the rhizosphere of maize grown in red soils, which were derived from four long-term fertilization regimes. Root-free rhizosphere soil samples were separated into three aggregate fractions whereby the abundance and community composition were examined for nematode and total bacterial communities. A functional group of alkaline phosphomonoesterase (ALP) producing bacteria was included to test the hypothesis that nematode grazing may significantly affect specific bacteria-mediated ecological functions, that is, organic phosphate cycling in soil. Results of correlation analysis, structural equation modeling and interaction networks combined with laboratory microcosm experiments consistently indicated that bacterivorous nematodes enhanced bacterial diversity, and the abundance of bacterivores was positively correlated with bacterial biomass, including ALP-producing bacterial abundance. Significantly, such effects were more pronounced in large macroaggregates than in microaggregates. There was a positive correlation between the most dominant bacterivores Protorhabditis and the ALP-producing keystone 'species' Mesorhizobium. Taken together, these findings implicate important roles of nematodes in stimulating bacterial dynamics in a spatially dependent manner. PMID:28742069

Nematode grazing promotes bacterial community dynamics in soil at the aggregate level.

PubMed

Jiang, Yuji; Liu, Manqiang; Zhang, Jiabao; Chen, Yan; Chen, Xiaoyun; Chen, Lijun; Li, Huixin; Zhang, Xue-Xian; Sun, Bo

2017-12-01

Nematode predation has important roles in determining bacterial community composition and dynamics, but the extent of the effects remains largely rudimentary, particularly in natural environment settings. Here, we investigated the complex microbial-microfaunal interactions in the rhizosphere of maize grown in red soils, which were derived from four long-term fertilization regimes. Root-free rhizosphere soil samples were separated into three aggregate fractions whereby the abundance and community composition were examined for nematode and total bacterial communities. A functional group of alkaline phosphomonoesterase (ALP) producing bacteria was included to test the hypothesis that nematode grazing may significantly affect specific bacteria-mediated ecological functions, that is, organic phosphate cycling in soil. Results of correlation analysis, structural equation modeling and interaction networks combined with laboratory microcosm experiments consistently indicated that bacterivorous nematodes enhanced bacterial diversity, and the abundance of bacterivores was positively correlated with bacterial biomass, including ALP-producing bacterial abundance. Significantly, such effects were more pronounced in large macroaggregates than in microaggregates. There was a positive correlation between the most dominant bacterivores Protorhabditis and the ALP-producing keystone 'species' Mesorhizobium. Taken together, these findings implicate important roles of nematodes in stimulating bacterial dynamics in a spatially dependent manner.

Protein aggregation as bacterial inclusion bodies is reversible.

PubMed

Carrió, M M; Villaverde, A

2001-01-26

Inclusion bodies are refractile, intracellular protein aggregates usually observed in bacteria upon targeted gene overexpression. Since their occurrence has a major economical impact in protein production bio-processes, in vitro refolding strategies are under continuous exploration. In this work, we prove spontaneous in vivo release of both beta-galactosidase and P22 tailspike polypeptides from inclusion bodies resulting in their almost complete disintegration and in the concomitant appearance of soluble, properly folded native proteins with full biological activity. Since, in particular, the tailspike protein exhibits an unusually slow and complex folding pathway involving deep interdigitation of beta-sheet structures, its in vivo refolding indicates that bacterial inclusion body proteins are not collapsed into an irreversible unfolded state. Then, inclusion bodies can be observed as transient deposits of folding-prone polypeptides, resulting from an unbalanced equilibrium between in vivo protein precipitation and refolding that can be actively displaced by arresting protein synthesis. The observation that the formation of big inclusion bodies is reversible in vivo can be also relevant in the context of amyloid diseases, in which deposition of important amounts of aggregated protein initiates the pathogenic process.

Enhanced transformation of tetrabromobisphenol a by nitrifiers in nitrifying activated sludge.

PubMed

Li, Fangjie; Jiang, Bingqi; Nastold, Peter; Kolvenbach, Boris Alexander; Chen, Jianqiu; Wang, Lianhong; Guo, Hongyan; Corvini, Philippe François-Xavier; Ji, Rong

2015-04-07

The fate of the most commonly used brominated flame retardant, tetrabromobisphenol A (TBBPA), in wastewater treatment plants is obscure. Using a (14)C-tracer, we studied TBBPA transformation in nitrifying activated sludge (NAS). During the 31-day incubation, TBBPA transformation (half-life 10.3 days) was accompanied by mineralization (17% of initial TBBPA). Twelve metabolites, including those with single benzene ring, O-methyl TBBPA ether, and nitro compounds, were identified. When allylthiourea was added to the sludge to completely inhibit nitrification, TBBPA transformation was significantly reduced (half-life 28.9 days), formation of the polar and single-ring metabolites stopped, but O-methylation was not significantly affected. Abiotic experiments confirmed the generation of mono- and dinitro-brominated forms of bisphenol A in NAS by the abiotic nitration of TBBPA by nitrite, a product of ammonia-oxidizing microorganisms (AOMs). Three biotic (type II ipso-substitution, oxidative skeletal cleavage, and O-methylation) and one abiotic (nitro-debromination) pathways were proposed for TBBPA transformation in NAS. Apart from O-methylation, AOMs were involved in three other pathways. Our results are the first to provide information about the complex metabolism of TBBPA in NAS, and they are consistent with a determining role for nitrifiers in TBBPA degradation by initiating its cleavage into single-ring metabolites that are substrates for the growth of heterotrophic bacteria.

Oil-derived marine aggregates - hot spots of polysaccharide degradation by specialized bacterial communities

NASA Astrophysics Data System (ADS)

Arnosti, Carol; Ziervogel, Kai; Yang, Tingting; Teske, Andreas

2016-07-01

Aggregates generated in the laboratory from incubations of seawater and surface-water oil collected in the initial phase of the Deepwater Horizon oil spill resemble the oil-aggregates observed in situ. Here, we investigated the enzyme activities and microbial community composition of laboratory generated oil-aggregates, focusing on the abilities of these communities to degrade polysaccharides, which are major components of marine organic matter and are abundant constituents of exopolymeric substances (EPS) generated by oil-associated bacteria in response to the presence of oil. The patterns of polysaccharide-hydrolyzing enzyme activities in oil aggregates were very different from those in the water surrounding the aggregates after formation, and in the surface water that did not contain the oil. Specific oil aggregate-associated hydrolysis rates were also considerably higher than in the water surrounding the aggregates. The differences in initial hydrolysis profiles, and in evolution of these profiles with time, points to specialized metabolic abilities among the oil-aggregate communities compared to oil-water and ambient water communities. The composition of the oil-aggregate community indicates a multifunctional microbial assemblage containing primary oil-degrading and exopolysaccharide-producing members of the Gammaproteobacteria, and diverse members of the Alphaproteobacteria, Bacteroidetes and Planktomycetales that most likely participate in the breakdown of oil-derived bacterial biopolymers. Formation and aging of oil-aggregates encourages the growth and transformation of microbial communities that are specialized in degradation of petroleum, as well as their secondary degradation products.

Anammox enrichment from reject water on blank biofilm carriers and carriers containing nitrifying biomass: operation of two moving bed biofilm reactors (MBBR).

PubMed

Zekker, Ivar; Rikmann, Ergo; Tenno, Toomas; Lemmiksoo, Vallo; Menert, Anne; Loorits, Liis; Vabamäe, Priit; Tomingas, Martin; Tenno, Taavo

2012-07-01

The anammox bacteria were enriched from reject water of anaerobic digestion of municipal wastewater sludge onto moving bed biofilm reactor (MBBR) system carriers-the ones initially containing no biomass (MBBR1) as well as the ones containing nitrifying biomass (MBBR2). Duration of start-up periods of the both reactors was similar (about 100 days), but stable total nitrogen (TN) removal efficiency occurred earlier in the system containing nitrifying biomass. Anammox TN removal efficiency of 70% was achieved by 180 days in both 20 l volume reactors at moderate temperature of 26.0°C. During the steady state phase of operation of MBBRs the average TN removal efficiencies and maximum TN removal rates in MBBR1 were 80% (1,000 g-N/m(3)/day, achieved by 308 days) and in MBBR2 85% (1,100 g-N/m(3)/day, achieved by 266 days). In both reactors mixed bacterial cultures were detected. Uncultured Planctomycetales bacterium clone P4, Candidatus Nitrospira defluvii and uncultured Nitrospira sp. clone 53 were identified by PCR-DGGE from the system initially containing blank biofilm carriers as well as from the nitrifying biofilm system; from the latter in addition to these also uncultured ammonium oxidizing bacterium clone W1 and Nitrospira sp. clone S1-62 were detected. FISH analysis revealed that anammox microorganisms were located in clusters in the biofilm. Using previously grown nitrifying biofilm matrix for anammox enrichment has some benefits over starting up the process from zero, such as less time for enrichment and protection against severe inhibitions in case of high substrate loading rates.

Nitrifying biomass characterization and monitoring during bioaugmentation in a membrane bioreactor.

PubMed

D'Anteo, Sibilla; Mannucci, Alberto; Meliani, Matteo; Verni, Franco; Petroni, Giulio; Munz, Giulio; Lubello, Claudio; Mori, Gualtiero; Vannini, Claudia

2015-01-01

A membrane bioreactor (MBR), fed with domestic wastewater, was bioaugmented with nitrifying biomass selected in a side-stream MBR fed with a synthetic high nitrogen-loaded influent. Microbial communities evolution was monitored and comparatively analysed through an extensive bio-molecular investigation (16S rRNA gene library construction and terminal-restriction fragment length polymorphism techniques) followed by statistical analyses. As expected, a highly specialized nitrifying biomass was selected in the side-stream reactor fed with high-strength ammonia synthetic wastewater. The bioaugmentation process caused an increase of nitrifying bacteria of the genera Nitrosomonas (up to more than 30%) and Nitrobacter in the inoculated MBR reactor. The overall structure of the microbial community changed in the mainstream MBR as a result of bioaugmentation. The effect of bioaugmentation in the shift of the microbial community was also verified through statistical analysis.

Visualizing tributyltin (TBT) in bacterial aggregates by specific rhodamine-based fluorescent probes.

PubMed

Jin, Xilang; Hao, Likai; She, Mengyao; Obst, Martin; Kappler, Andreas; Yin, Bing; Liu, Ping; Li, Jianli; Wang, Lanying; Shi, Zhen

2015-01-01

Here we present the first examples of fluorescent and colorimetric probes for microscopic TBT imaging. The fluorescent probes are highly selective and sensitive to TBT and have successfully been applied for imaging of TBT in bacterial Rhodobacter ferrooxidans sp. strain SW2 cell-EPS-mineral aggregates and in cell suspensions of the marine cyanobacterium Synechococcus PCC 7002 by using confocal laser scanning microscopy. Copyright © 2014 Elsevier B.V. All rights reserved.

In Situ Identification and Stratification of Monochloramine Inhibition Effects on Nitrifying Biofilms as Determined by the Use of Microelectrodes

EPA Science Inventory

The nitrifying biofilm grown in an annular biofilm reactor and the microbial deactivation achieved after monochloramine treatment were investigated using microelectrodes. The nitrifying biofilm ammonium microprofile was measured and the effect of monochloramine on nitrifying bio...

Establishment and Early Succession of Bacterial Communities in Monochloramine-Treated Drinking Water Biofilms

EPA Science Inventory

Monochloramine is increasingly used as a drinking water disinfectant because it forms lower levels of regulated disinfection by-products. While its use has been shown to increase nitrifying bacteria, little is known about the bacterial succession within biofilms in monochloramin...

Comparative analysis of nitrifying bacteria in full-scale oxidation ditch and aerated nitrification biofilter by using fluorescent in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE).

PubMed

Mertoglu, Bulent; Calli, Baris; Girgin, Emine; Inanc, Bulent; Ozturk, Izzet

2005-01-01

In this study, nitrification performances and composition of nitrifying populations in a full-scale oxidation ditch and a high-rate submerged media nitrification biofilter were comparatively analyzed. In addition to different reactor configurations, effects of differing operational conditions on the nitrification efficiency and bacterial diversity were also explored and evaluated thoroughly. In microbial analysis of sludge samples fluorescent in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE) techniques were used complementary to each other. The extended aeration oxidation ditch subjected to the study is operated as a nitrogen and phosphorus removal system consisting of anaerobic, anoxic, and aerobic zones. The high-rate submerged media aerated filter is operated as nitrification step following the conventional activated sludge unit and the nitrified wastewater is discharged to the sea without complete nitrogen removal. In situ hybridization results have indicated that Nitrosomonas-like ammonia oxidizing and Nitrospira-related nitrite oxidizing bacteria were intensively present in vigorous flocs in nitrification biofilter while carbonaceous bacteria belong to beta subclass of Proteobacteria were considerably dominant in oxidation ditch. Low quantities of nitrifiers in oxidation ditch were also confirmed by the dissimilarity in intensive bands between two systems obtained with DGGE analysis.

Post carbon removal nitrifying MBBR operation at high loading and exposure to starvation conditions.

PubMed

Young, Bradley; Delatolla, Robert; Kennedy, Kevin; LaFlamme, Edith; Stintzi, Alain

2017-09-01

This study investigates the performance of MBBR nitrifying biofilm post carbon removal at high loading and starvation conditions. The nitrifying MBBR, treating carbon removal lagoon effluent, achieved a maximum SARR of 2.13gN/m 2 d with complete conversion of ammonia to nitrate. The results also show the MBBR technology is capable of maintaining a stable biofilm under starvation conditions in systems that nitrify intermittently. The biomass exhibited a higher live fraction of total cells in the high loaded reactors (73-100%) as compared to the reactors operated in starvation condition (26-82%). For both the high loaded and starvation condition, the microbial communities significantly changed with time of operation. The nitrifying community, however, remained steady with the family Nitrosomonadacea as the primary AOBs and Nitrospira as the primary NOB. During starvation conditions, the relative abundance of AOBs decreased and Nitrospira increased corresponding to an NOB/AOB ratio of 5.2-12.1. Copyright © 2017 Elsevier Ltd. All rights reserved.

Influence of water quality on nitrifier regrowth in two full-scale drinking water distribution systems.

PubMed

Scott, Daniel B; Van Dyke, Michele I; Anderson, William B; Huck, Peter M

2015-12-01

The potential for regrowth of nitrifying microorganisms was monitored in 2 full-scale chloraminated drinking water distribution systems in Ontario, Canada, over a 9-month period. Quantitative PCR was used to measure amoA genes from ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), and these values were compared with water quality parameters that can influence nitrifier survival and growth, including total chlorine, ammonia, temperature, pH, and organic carbon. Although there were no severe nitrification episodes, AOB and AOA were frequently detected at low concentrations in samples collected from both distribution systems. A culture-based presence-absence test confirmed the presence of viable nitrifiers. AOB were usually present in similar or greater numbers than AOA in both systems. As well, AOB showed higher regrowth potential compared with AOA in both systems. Statistically significant correlations were measured between several water quality parameters of relevance to nitrification. Total chlorine was negatively correlated with both nitrifiers and heterotrophic plate count (HPC) bacteria, and ammonia levels were positively correlated with nitrifiers. Of particular importance was the strong correlation between HPC and AOB, which reinforced the usefulness of HPC as an operational parameter to measure general microbiological conditions in distribution systems.

The effects of salinity on nitrification using halophilic nitrifiers in a Sequencing Batch Reactor treating hypersaline wastewater.

PubMed

Cui, You-Wei; Zhang, Hong-Yu; Ding, Jie-Ran; Peng, Yong-Zhen

2016-04-25

With annual increases in the generation and use of saline wastewater, the need to avoid environmental problems such as eutrophication is critical. A previous study identified ways to start up a halophilic sludge domesticated from estuarine sediments to remove nitrogen from wastewater with a salinity of 30 g/L. This investigation expands that work to explore the impact of salinity on nitrogen removal. This study demonstrated that the mixed halophilic consortia removed nitrogen from wastewater with a salinity of 30-85 g/L. A kinetic analysis showed that halophilic nitrifiers selected based on hypersalinity were characterized by low Ks, μmax and specific ammonium oxidization rates. This explains the decrease in ammonium removal efficiency in the high salinity operational phases. Salinity inhibited ammonia oxidizing bacteria (AOB) activity, as well as the number of dominant AOB, but did not significantly affect the AOB dominant species. Three most dominant AOB lineages in the halophilic sludge were Nitrosomonas marina, Nitrosomonas europaea, and Nitrosococcus mobilis. Nitrosomonas europaea and Nitrosococcus mobilis were mainly affected by salinity, while nitrite accumulation and ammonia loading played the key role in determining the abundance of Nitrosococcus mobilis and Nitrosococcus europaea. The study contributes insights about shifts in halophilic nitrifying bacterial populations.

The effects of salinity on nitrification using halophilic nitrifiers in a Sequencing Batch Reactor treating hypersaline wastewater

PubMed Central

Cui, You-Wei; Zhang, Hong-Yu; Ding, Jie-Ran; Peng, Yong-Zhen

2016-01-01

With annual increases in the generation and use of saline wastewater, the need to avoid environmental problems such as eutrophication is critical. A previous study identified ways to start up a halophilic sludge domesticated from estuarine sediments to remove nitrogen from wastewater with a salinity of 30 g/L. This investigation expands that work to explore the impact of salinity on nitrogen removal. This study demonstrated that the mixed halophilic consortia removed nitrogen from wastewater with a salinity of 30–85 g/L. A kinetic analysis showed that halophilic nitrifiers selected based on hypersalinity were characterized by low Ks, μmax and specific ammonium oxidization rates. This explains the decrease in ammonium removal efficiency in the high salinity operational phases. Salinity inhibited ammonia oxidizing bacteria (AOB) activity, as well as the number of dominant AOB, but did not significantly affect the AOB dominant species. Three most dominant AOB lineages in the halophilic sludge were Nitrosomonas marina, Nitrosomonas europaea, and Nitrosococcus mobilis. Nitrosomonas europaea and Nitrosococcus mobilis were mainly affected by salinity, while nitrite accumulation and ammonia loading played the key role in determining the abundance of Nitrosococcus mobilis and Nitrosococcus europaea. The study contributes insights about shifts in halophilic nitrifying bacterial populations. PMID:27109617

Marine bacterial degradation of brominated methanes

USGS Publications Warehouse

Goodwin, K.D.; Lidstrom, M.E.; Oremland, R.S.

1997-01-01

Brominated methanes are ozone-depleting compounds whose natural sources include marine algae such as kelp. Brominated methane degradation by bacteria was investigated to address whether bacterial processes might effect net emission of these compounds to the atmosphere. Bacteria in seawater collected from California kelp beds degraded CH2Br2 but not CHBr3. Specific inhibitors showed that methanotrophs and nitrifiers did not significantly contribute to CH2Br2 removal. A seawater enrichment culture oxidized 14CH2Br2 to 14CO2 as well as 14CH3Br to 14CO2. The rates of CH2Br2 degradation in laboratory experiments suggest that bacterial degradation of CH2Br2 in a kelp bed accounts for <1% of the CH2Br2 produced by the kelp. However, the half-life of CH2Br2 due to bacterial removal appears faster than hydrolysis and within an order of magnitude of volatilization to the atmosphere.Brominated methanes are ozone-depleting compounds whose natural sources include marine algae such as kelp. Brominated methane degradation by bacteria was investigated to address whether bacterial processes might effect net emission of these compounds to the atmosphere. Bacteria in seawater collected from California kelp beds degraded CH2Br2 but not CHBr3. Specific inhibitors showed that methanotrophs and nitrifiers did not significantly contribute to CH2Br2 removal. A seawater enrichment culture oxidized 14CH2Br2 to 14CO2 as well as 14CH3Br to 14CO2. The rates of CH2Br2 degradation in laboratory experiments suggest that bacterial degradation of CH2Br2 in a kelp bed accounts for <1% of the CH2Br2 produced by the kelp. However, the half-life of CH2Br2 due to bacterial removal appears faster than hydrolysis and within an order of magnitude of volatilization to the atmosphere.

Low-Dissolved-Oxygen Nitrifying Systems Exploit Ammonia-Oxidizing Bacteria with Unusually High Yields▿

PubMed Central

Bellucci, Micol; Ofiţeru, Irina D.; Graham, David W.; Head, Ian M.; Curtis, Thomas P.

2011-01-01

In wastewater treatment plants, nitrifying systems are usually operated with elevated levels of aeration to avoid nitrification failures. This approach contributes significantly to operational costs and the carbon footprint of nitrifying wastewater treatment processes. In this study, we tested the effect of aeration rate on nitrification by correlating ammonia oxidation rates with the structure of the ammonia-oxidizing bacterial (AOB) community and AOB abundance in four parallel continuous-flow reactors operated for 43 days. Two of the reactors were supplied with a constant airflow rate of 0.1 liter/min, while in the other two units the airflow rate was fixed at 4 liters/min. Complete nitrification was achieved in all configurations, though the dissolved oxygen (DO) concentration was only 0.5 ± 0.3 mg/liter in the low-aeration units. The data suggest that efficient performance in the low-DO units resulted from elevated AOB levels in the reactors and/or putative development of a mixotrophic AOB community. Denaturing gel electrophoresis and cloning of AOB 16S rRNA gene fragments followed by sequencing revealed that the AOB community in the low-DO systems was a subset of the community in the high-DO systems. However, in both configurations the dominant species belonged to the Nitrosomonas oligotropha lineage. Overall, the results demonstrated that complete nitrification can be achieved at low aeration in lab-scale reactors. If these findings could be extended to full-scale plants, it would be possible to minimize the operational costs and greenhouse gas emissions without risk of nitrification failure. PMID:21926211

Performance and Biofilm Activity of Nitrifying Biofilters Removing Trihalomethanes

EPA Science Inventory

Nitrifying biofilters seeded with three different mixed-culture sources degraded trichloromethane (TCM) and dibromochloromethane (DBCM). In addition, resuspended biofilm degraded TCM, bromododichloromethane (BDCM), DBCM, and tribromomethane (TBM) in backwash batch kinetic tests,...

Effects of Grazing by Flagellates on Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Chemostats

PubMed Central

Verhagen, Frank J. M.; Laanbroek, Hendrikus J.

1992-01-01

The enhanced mineralization of organic nitrogen by bacteriophagous protozoa is thought to favor the nitrification process in soils, in which nitrifying bacteria have to compete with heterotrophic bacteria for the available ammonium. To obtain more insight into this process, the influence of grazing by the bacteriovorous flagellate Adriamonas peritocrescens on the competition for limiting amounts of ammonium between the ammonium-oxidizing species Nitrosomonas europaea and the heterotrophic species Arthrobacter globiformis was studied in the presence of Nitrobacter winogradskyi in continuous cultures at dilution rates of 0.004 and 0.01 h-1. The ammonium concentration in the reservoir was maintained at 2 mM, whereas the glucose concentration was increased stepwise from 0 to 7 mM. A. globiformis won the competition for limiting amounts of ammonium when the glucose concentration in the reservoirs increased, in agreement with previously described experiments in which the flagellates were not included. The numbers of nitrifying bacteria decreased as the numbers of heterotrophic bacteria rose with increasing glucose concentrations. Critical C/N ratios, i.e., ratios between glucose and ammonium in the reservoirs at which no nitrate was found in the culture vessels, of 12.5 and 10.5 were determined at dilution rates of 0.004 and 0.01 h-1, respectively. Below these critical values, coexistence of the competing species was found. The numbers of nitrifying bacteria decreased more in the presence of flagellates than in their absence, presumably by selective predation on the nitrifying bacteria, either in the liquid culture or on the glass wall of the culture vessels. Despite this, the rate of nitrate production did not decrease more in the presence of flagellates than in their absence. This demonstrates that no correlation has to be expected between numbers of nitrifying bacteria and their activity and that a constant nitrification rate per cell cannot be assumed for nitrifying

Biological removal of the xenobiotic trichloroethylene (TCE) through cometabolism in nitrifying systems.

PubMed

Kocamemi, B Alpaslan; Ceçen, F

2010-01-01

In the present study, cometabolic TCE degradation was evaluated using NH(4)-N as the growth-substrate. At initial TCE concentrations up to 845 microg/L, TCE degradation followed first-order kinetics. The increase in ammonium utilization rate favored the degradation of TCE. This ensured that biological transformation of TCE in nitrifying systems is accomplished through a cometabolic pathway by the catalysis of non-specific ammonia oxygenase enzyme of nitrifiers. The transformation yield (T(y)) of TCE, the amount of TCE degraded per unit mass of NH(4)-N, strongly depended on the initial NH(4)-N and TCE concentrations. In order to allow a rough estimation of TCE removal and nitrification at different influent TCE and NH(4)-N concentrations, a linear relationship was developed between 1/T(y) and the initial NH(4)-N/TCE ratio. The estimated T(y) values lead to the conclusion that nitrifying systems are promising candidates for biological removal of TCE through cometabolism.

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.

PubMed

Koslicki, David; Chatterjee, Saikat; Shahrivar, Damon; Walker, Alan W; Francis, Suzanna C; Fraser, Louise J; Vehkaperä, Mikko; Lan, Yueheng; Corander, Jukka

2015-01-01

Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of such large datasets is challenging. There has been a recent surge of interest in using compressed sensing inspired and convex-optimization based methods to solve the estimation problem for bacterial community composition. These methods typically rely on summarizing the sequence data by frequencies of low-order k-mers and matching this information statistically with a taxonomically structured database. Here we show that the accuracy of the resulting community composition estimates can be substantially improved by aggregating the reads from a sample with an unsupervised machine learning approach prior to the estimation phase. The aggregation of reads is a pre-processing approach where we use a standard K-means clustering algorithm that partitions a large set of reads into subsets with reasonable computational cost to provide several vectors of first order statistics instead of only single statistical summarization in terms of k-mer frequencies. The output of the clustering is then processed further to obtain the final estimate for each sample. The resulting method is called Aggregation of Reads by K-means (ARK), and it is based on a statistical argument via mixture density formulation. ARK is found to improve the fidelity and robustness of several recently introduced methods, with only a modest increase in computational complexity. An open source, platform-independent implementation of the method in the Julia programming language is freely available at https://github.com/dkoslicki/ARK. A Matlab implementation is available at http://www.ee.kth.se/ctsoftware.

Monochloramine Cometabolism by Nitrifying Biofilm Relevant to Drinking Water

EPA Science Inventory

Recently, biological monochloramine removal (i.e., cometabolism) by a pure culture ammonia–oxidizing bacteria, Nitrosomonas europaea, and a nitrifying mixed–culture have been shown to increase monochloramine demand. Although important, these previous suspended culture batch kine...

Development of Denitrifying and Nitrifying Bacteria and Their Co-occurrence in Newly Created Biofilms in Urban Streams

NASA Astrophysics Data System (ADS)

Vaessen, T. N.; Martí Roca, E.; Pinay, G.; Merbt, S. N.

2015-12-01

Biofilms play a pivotal role on nutrient cycling in streams, which ultimately dictates the export of nutrients to downstream ecosystems. The extent to which biofilms influence the concentration of dissolved nutrients, oxygen and pH in the water column may be determined by the composition of the microbial assemblages and their activity. Evidence of biological interactions among bacteria and algae are well documented. However, the development, succession and co-occurence of nitrifying and denitrifying bacteria remain poorly understood. These bacteria play a relevant role on the biogeochemical process associated to N cycling, and their relative abundance can dictate the fate of dissolved inorganic nitrogen in streams. In particular, previous studies indicated that nitrifiers are enhanced in streams receiving inputs from wastewater treatment plant (WWTP) effluents due to both increases in ammonium concentration and inputs of nitrifiers. However, less is known about the development of denitrifiers in receiving streams, although environmental conditions seem to favor it. We conducted an in situ colonization experiment in a stream receiving effluent from a WWTP to examine how this input influences the development and co-occurrence of nitrifying and denitrifying bacteria. We placed artificial substrata at different locations relative to the effluent and sampled them over time to characterize the developed biofilm in terms of bulk measurements (organic matter content and algae) as well as in terms of abundance of nitrifiers and denitrifiers (using qPCR). The results of this study contribute to a better understanding of the temporal dynamics of denitrifiers and nitrifiers in relation to the developed organic matter, dissolved oxygen and pH and the biomass accrual in stream biofilms under the influence of nutrients inputs from WWTP effluent. Ultimately, the results provide insights on the potential role of nitrifiers and denitrifiers on N cycling in WWTP effluent receiving

Effects of elevated CO2 concentrations on denitrifying and nitrifying popualtions at terrestrial CO2 leakeage analogous sites

NASA Astrophysics Data System (ADS)

Christine, Dictor Marie; Catherine, Joulian; Valerie, Laperche; Stephanie, Coulon; Dominique, Breeze

2010-05-01

CO2 capture and geological storage (CCS) is recognized to be an important option for carbon abatement in Europe. One of the risks of CCS is the leakage from storage site. A laboratory was conducted on soil samples sampled near-surface from a CO2 leakage analogous site (Latera, Italy) in order to evaluate the impact of an elevated soil CO2 concentration on terrestrial bacterial ecosystems form near surface terrestrial environments and to determine a potential bacterial indicator of CO2 leakage from storage site. Surveys were conducted along a 50m long transect across the vent centre, providing a spectrum of CO2 flux rates, soil gas concentrations and compositions (Beaubien et al., 2007). A bacterial diversity studies, performed by CE-SSCP technique, on a soil profile with increasing CO2 soil concentrations (from 0.3% to 100%) showed that a change on bacterial diversity was noted when CO2 concentration was above 50 % of CO2. From this result, 3 soil samples were taken at 70 cm depth in 3 distinct zones (background soil CO2 content, soil CO2 content of 20% and soil CO2 content of 50%). Then theses soil samples were incubated under closed jars flushed with different air atmospheres (20, 50 and 90 % of CO2) during 18 months. At initial, 3, 6, 12 and 18 months, some soil samples were collected in order to estimate the denitrifying, nitrifying activities as a function of CO2 concentration content and times. Theses enzymatic activities were chosen because one occurs under anaerobic conditions (denitrification) and the other occurs under aerobic conditions (nitrification). Both of them were involved in the nitrogen cycle and are major actors of soil function and groundwater quality preservation. Metabolic diversity using BIOLOG Ecoplates was determined on every soil samples. Physico-chemical parameters (e.g. pH, bulk chemistry, mineralogy) were analyzed to have some information about the evolution of the soil during the incubation with increasing soil CO2 concentrations

Nitrification and occurrence of salt-tolerant nitrifying bacteria in the Negev desert soils.

PubMed

Nejidat, Ali

2005-03-01

Ammonia oxidation potential, major ammonia oxidizers and occurrence of salt-tolerant nitrifying bacteria were studied in soil samples collected from diverse ecosystems along the northern Negev desert. Great diversity in ammonia oxidation potential was observed among the soil samples, and ammonia oxidizers were the rate-limiting step of nitrification. Denaturing gradient gel electrophoresis and partial 16S rRNA gene sequences indicate that members of the genus Nitrosospira are the major ammonia oxidizers in the natural desert soil samples. Upon enrichment with different salt concentrations, salt-tolerant nitrifying enrichments were established from several soil samples. In two enrichments, nitrification was not inhibited by 400 mM NaCl. Electrophoretic analysis and partial 16S rRNA gene sequences indicate that Nitrosomonas species were dominant in the 400 mM salt enrichment. The results point towards the potential of the desert ecosystem as a source of stress-tolerant nitrifying bacteria or other microorganisms with important properties.

Close association of active nitrifiers with Beggiatoa mats covering deep-sea hydrothermal sediments.

PubMed

Winkel, Matthias; de Beer, Dirk; Lavik, Gaute; Peplies, Jörg; Mußmann, Marc

2014-06-01

Hydrothermal sediments in the Guaymas Basin are covered by microbial mats that are dominated by nitrate-respiring and sulphide-oxidizing Beggiatoa. The presence of these mats strongly correlates with sulphide- and ammonium-rich fluids venting from the subsurface. Because ammonium and oxygen form opposed gradients at the sediment surface, we hypothesized that nitrification is an active process in these Beggiatoa mats. Using biogeochemical and molecular methods, we measured nitrification and determined the diversity and abundance of nitrifiers. Nitrification rates ranged from 74 to 605 μmol N l(-1)  mat day(-1), which exceeded those previously measured in hydrothermal plumes and other deep-sea habitats. Diversity and abundance analyses of archaeal and bacterial ammonia monooxygenase subunit A genes, archaeal 16S ribosomal RNA pyrotags and fluorescence in situ hybridization confirmed that ammonia- and nitrite-oxidizing microorganisms were associated with Beggiatoa mats. Intriguingly, we observed cells of bacterial and potential thaumarchaeotal ammonia oxidizers attached to narrow, Beggiatoa-like filaments. Such a close spatial coupling of nitrification and nitrate respiration in mats of large sulphur bacteria is novel and may facilitate mat-internal cycling of nitrogen, thereby reducing loss of bioavailable nitrogen in deep-sea sediments. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Relative contribution of ammonia oxidizing bacteria and other members of nitrifying activated sludge communities to micropollutant biotransformation.

PubMed

Men, Yujie; Achermann, Stefan; Helbling, Damian E; Johnson, David R; Fenner, Kathrin

2017-02-01

Improved micropollutant (MP) biotransformation during biological wastewater treatment has been associated with high ammonia oxidation activities, suggesting co-metabolic biotransformation by ammonia oxidizing bacteria as an underlying mechanism. The goal of this study was to clarify the contribution of ammonia oxidizing bacteria to increased MP degradation in nitrifying activated sludge (NAS) communities using a series of inhibition experiments. To this end, we treated a NAS community with two different ammonia oxidation inhibitors, namely octyne (OCT), a mechanistic inhibitor that covalently binds to ammonia monooxygenases, and allylthiourea (ATU), a copper chelator that depletes copper ions from the active center of ammonia monooxygenases. We investigated the biotransformation of 79 structurally different MPs by the inhibitor-treated and untreated sludge communities. Fifty-five compounds exhibited over 20% removal in the untreated control after a 46 h-incubation. Of these, 31 compounds were significantly inhibited by either ATU and/or OCT. For 17 of the 31 MPs, the inhibition by ATU at 46 h was substantially higher than by OCT despite the full inhibition of ammonia oxidation by both inhibitors. This was particularly the case for almost all thioether and phenylurea compounds tested, suggesting that in nitrifying activated sludge communities, ATU does not exclusively act as an inhibitor of bacterial ammonia oxidation. Rather, ATU also inhibited enzymes contributing to MP biotransformation but not to bulk ammonia oxidation. Thus, inhibition studies with ATU tend to overestimate the contribution of ammonia-oxidizing bacteria to MP biotransformation in nitrifying activated sludge communities. Biolog tests revealed only minor effects of ATU on the heterotrophic respiration of common organic substrates by the sludge community, suggesting that ATU did not affect enzymes that were essential in energy conservation and central metabolism of heterotrophs. By comparing ATU

Relative rates of nitric oxide and nitrous oxide production by nitrifiers, denitrifiers, and nitrate respirers

NASA Technical Reports Server (NTRS)

Anderson, I. C.; Levine, J. S.

1986-01-01

An account is given of the atmospheric chemical and photochemical effects of biogenic nitric and nitrous oxide emissions. The magnitude of the biogenic emission of NO is noted to remain uncertain. Possible soil sources of NO and N2O encompass nitrification by autotropic and heterotropic nitrifiers, denitrification by nitrifiers and denitrifiers, nitrate respiration by fermenters, and chemodenitrification. Oxygen availability is the primary determinant of these organisms' relative rates of activity. The characteristics of this major influence are presently investigated in light of the effect of oxygen partial pressure on NO and N2O production by a wide variety of common soil-nitrifying, denitrifying, and nitrate-respiring bacteria under laboratory conditions. The results obtained indicate that aerobic soils are primary sources only when there is sufficient moisture to furnish anaerobic microsites for denitrification.

Anti-Pseudomonas aeruginosa IgY Antibodies Induce Specific Bacterial Aggregation and Internalization in Human Polymorphonuclear Neutrophils

PubMed Central

Thomsen, K.; Christophersen, L.; Bjarnsholt, T.; Jensen, P. Ø.; Moser, C.

2015-01-01

Polymorphonuclear neutrophils (PMNs) are essential cellular constituents in the innate host response, and their recruitment to the lungs and subsequent ubiquitous phagocytosis controls primary respiratory infection. Cystic fibrosis pulmonary disease is characterized by progressive pulmonary decline governed by a persistent, exaggerated inflammatory response dominated by PMNs. The principal contributor is chronic Pseudomonas aeruginosa biofilm infection, which attracts and activates PMNs and thereby is responsible for the continuing inflammation. Strategies to prevent initial airway colonization with P. aeruginosa by augmenting the phagocytic competence of PMNs may postpone the deteriorating chronic biofilm infection. Anti-P. aeruginosa IgY antibodies significantly increase the PMN-mediated respiratory burst and subsequent bacterial killing of P. aeruginosa in vitro. The mode of action is attributed to IgY-facilitated formation of immobilized bacteria in aggregates, as visualized by fluorescence microscopy and the induction of increased bacterial hydrophobicity. Thus, the present study demonstrates that avian egg yolk immunoglobulins (IgY) targeting P. aeruginosa modify bacterial fitness, which enhances bacterial killing by PMN-mediated phagocytosis and thereby may facilitate a rapid bacterial clearance in airways of people with cystic fibrosis. PMID:25895968

Monochloramine Cometabolism by Mixed-Culture Nitrifiers under Drinking Water Conditions

EPA Science Inventory

The current research investigated monochloramine cometabolism by nitrifying mixed cultures grown under drinking water relevant conditions and harvested from sand-packed reactors before conducting suspended growth batch kinetic experiments. Three batch reactors were used in each ...

Bioaugmentation of rapid sand filters by microbiome priming with a nitrifying consortium will optimize production of drinking water from groundwater.

PubMed

Albers, Christian Nyrop; Ellegaard-Jensen, Lea; Hansen, Lars Hestbjerg; Sørensen, Sebastian R

2018-02-01

Ammonium oxidation to nitrite and then to nitrate (nitrification) is a key process in many waterworks treating groundwater to make it potable. In rapid sand filters, nitrifying microbial communities may evolve naturally from groundwater bacteria entering the filters. However, in new filters this may take several months, and in some cases the nitrification process is never sufficiently rapid to be efficient or is only performed partially, with nitrite as an undesired end product. The present study reports the first successful priming of nitrification in a rapid sand filter treating groundwater. It is shown that nitrifying communities could be enriched by microbiomes from well-functioning rapid sand filters in waterworks and that the enriched nitrifying consortium could be used to inoculate fresh filters, significantly shortening the time taken for the nitrification process to start. The key nitrifiers in the enrichment were different from those in the well-functioning filter, but similar to those that initiated the nitrification process in fresh filters without inoculation. Whether or not the nitrification was primed with the enriched nitrifying consortium, the bacteria performing the nitrification process during start-up appeared to be slowly outcompeted by Nitrospira, the dominant nitrifying bacterium in well-functioning rapid sand filters. Copyright © 2017 Elsevier Ltd. All rights reserved.

Emergent macrophytes select for nitrifying and denitrifying microorganisms in constructed wetlands

NASA Astrophysics Data System (ADS)

Trias, Rosalia; Ramió Pujol, Sara; Bañeras, Lluis

2014-05-01

The use of constructed wetlands for wastewater treatment is a reliable low-cost alternative that has been widely developed during the last years. Several processes involving plants, sediments, and microbial communities contribute to nitrogen removal in wetlands. Vegetation plays an important role in this process, not only by nutrient assimilation but also by the stimulation of the plant associated microbiota. Plants supply oxygen at the close proximity of the root surface that may favour ammonia oxidizers. At the same time, exudation of organic compounds potentially speeds-up denitrification in the anoxic environment. The aim of this work was to understand the plant-microbe interactions at the root level in the Empuriabrava free water surface constructed wetland (Spain). The roots of the macrophytes Typha latifolia, Typha angustifolia, Phragmites australis and Bolboschoenus maritimus were sampled at four dates from January to September 2012, covering all the stages of plant growth. Additionally, sediment surrounding vegetation and non-vegetated sediments were sampled. Microbial community structure was analysed by pyrosequencing of bacterial and archaeal 16S rDNA and functional genes (nirK, nirS, nosZ and amoA). Bacterial communities were significantly different in sediments of the vegetated areas compared to the root surface. Plant roots exhibited a higher proportion of proteobacteria whereas Actinobacteria were dominant in sediments. The nitrifiers Nitrosomonas sp. and Nitrosococcus sp. accounted for less than 1% of all sequences. Archaeal communities were dominated by the Miscellaneous Crenarchaeotic Groups C2 and C3 and Methanomicrobia. Higher relative abundances of MCG were found in roots of P. australis, B. maritimus and T. angustifolia. Ammonia oxidizing archaea accounted for less than 0.1% of all sequences but were consistently more abundant in sediment samples compared to roots. NirK and NirS-type bacterial communities showed clearly distinct distribution

Variability of nitrifying communities in surface coastal waters of the Eastern South Pacific (∼36° S).

PubMed

Levipan, Héctor A; Molina, Verónica; Anguita, Cristóbal; Rain-Franco, Angel; Belmar, Lucy; Fernandez, Camila

2016-08-03

We report the seasonal and single-diurnal variability of potentially active members of the prokaryote community in coastal surface waters off central Chile and the relationship between nitrifiers and solar radiation by combining 16S cDNA-based pyrosequencing, RT-qPCR of specific gene markers for nitrifiers (amoA, for general AOA, AOA-A, AOA-B, Nitrosopumilus maritimus and beta-AOB; and 16S rRNA gene for Nitrospina-like NOB), and solar irradiance measurements. We also evaluated the effects of artificial UVA-PAR and PAR spectra on nitrifiers by RT-qPCR. All nitrifiers (except AOA-B ecotype) were detected via RT-qPCR but AOA was the only group detected by pyrosequencing. Results showed high variability in their transcriptional levels during the day which could be associated to sunlight intensity thresholds in winter although AOA and Nitrospina-like NOB transcript number were also potentially related with environmental substrate availability. Only N. maritimus amoA transcripts showed a significant negative correlation with solar irradiances in both periods. During spring-summer, Nitrospina transcripts decreased at higher sunlight intensities, whereas the opposite was found during winter under natural (in situ) and artificial light experiments. In summary, a nitrifying community with variable tolerance to solar radiation is responsible for daily nitrification, and was particularly diverse during winter in the study area. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Modelling cometabolic biotransformation of organic micropollutants in nitrifying reactors.

PubMed

Fernandez-Fontaina, E; Carballa, M; Omil, F; Lema, J M

2014-11-15

Cometabolism is the ability of microorganisms to degrade non-growth substrates in the presence of primary substrates, being the main removal mechanism behind the biotransformation of organic micropollutants in wastewater treatment plants. In this paper, a cometabolic Monod-type kinetics, linking biotransformation of micropollutants with primary substrate degradation, was applied to a highly enriched nitrifying activated sludge (NAS) reactor operated under different operational conditions (hydraulic retention time (HRT) and nitrifying activity). A dynamic model of the bioreactor was built taking into account biotransformation, sorption and volatilization. The micropollutant transformation capacity (Tc), the half-saturation constant (Ksc) and the solid-liquid partitioning coefficient (Kd) of several organic micropollutants were estimated at 25 °C using an optimization algorithm to fit experimental data to the proposed model with the cometabolic Monod-type biotransformation kinetics. The cometabolic Monod-type kinetic model was validated under different HRTs (1.0-3.7 d) and nitrification rates (0.12-0.45 g N/g VSS d), describing more accurately the fate of those compounds affected by the biological activity of nitrifiers (ibuprofen, naproxen, erythromycin and roxithromycin) compared to the commonly applied pseudo-first order micropollutant biotransformation kinetics, which does not link biotransformation of micropollutants to consumption of primary substrate. Furthermore, in contrast to the pseudo-first order biotransformation constant (k(biol)), the proposed cometabolic kinetic coefficients are independent of operational conditions such as the nitrogen loading rate applied. Also, the influence of the kinetic parameters on the biotransformation efficiency of NAS reactors, defined as the relative amount of the total inlet micropollutant load being biotransformed, was assessed considering different HRTs and nitrification rates. Copyright © 2014 Elsevier Ltd. All

Using Amplicon Sequencing To Characterize and Monitor Bacterial Diversity in Drinking Water Distribution Systems

PubMed Central

Shaw, Jennifer L. A.; Weyrich, Laura S.; Sawade, Emma; Drikas, Mary; Cooper, Alan J.

2015-01-01

Drinking water assessments use a variety of microbial, physical, and chemical indicators to evaluate water treatment efficiency and product water quality. However, these indicators do not allow the complex biological communities, which can adversely impact the performance of drinking water distribution systems (DWDSs), to be characterized. Entire bacterial communities can be studied quickly and inexpensively using targeted metagenomic amplicon sequencing. Here, amplicon sequencing of the 16S rRNA gene region was performed alongside traditional water quality measures to assess the health, quality, and efficiency of two distinct, full-scale DWDSs: (i) a linear DWDS supplied with unfiltered water subjected to basic disinfection before distribution and (ii) a complex, branching DWDS treated by a four-stage water treatment plant (WTP) prior to disinfection and distribution. In both DWDSs bacterial communities differed significantly after disinfection, demonstrating the effectiveness of both treatment regimes. However, bacterial repopulation occurred further along in the DWDSs, and some end-user samples were more similar to the source water than to the postdisinfection water. Three sample locations appeared to be nitrified, displaying elevated nitrate levels and decreased ammonia levels, and nitrifying bacterial species, such as Nitrospira, were detected. Burkholderiales were abundant in samples containing large amounts of monochloramine, indicating resistance to disinfection. Genera known to contain pathogenic and fecal-associated species were also identified in several locations. From this study, we conclude that metagenomic amplicon sequencing is an informative method to support current compliance-based methods and can be used to reveal bacterial community interactions with the chemical and physical properties of DWDSs. PMID:26162884

Crystal structure of the Haemophilus influenzae Hap adhesin reveals an intercellular oligomerization mechanism for bacterial aggregation

PubMed Central

Meng, Guoyu; Spahich, Nicole; Kenjale, Roma; Waksman, Gabriel; St Geme, Joseph W

2011-01-01

Bacterial biofilms are complex microbial communities that are common in nature and are being recognized increasingly as an important determinant of bacterial virulence. However, the structural determinants of bacterial aggregation and eventual biofilm formation have been poorly defined. In Gram-negative bacteria, a major subgroup of extracellular proteins called self-associating autotransporters (SAATs) can mediate cell–cell adhesion and facilitate biofilm formation. In this study, we used the Haemophilus influenzae Hap autotransporter as a prototype SAAT to understand how bacteria associate with each other. The crystal structure of the H. influenzae HapS passenger domain (harbouring the SAAT domain) was determined to 2.2 Å by X-ray crystallography, revealing an unprecedented intercellular oligomerization mechanism for cell–cell interaction. The C-terminal SAAT domain folds into a triangular-prism-like structure that can mediate Hap–Hap dimerization and higher degrees of multimerization through its F1–F2 edge and F2 face. The intercellular multimerization can give rise to massive buried surfaces that are required for overcoming the repulsive force between cells, leading to bacterial cell–cell interaction and formation of complex microcolonies. PMID:21841773

Effect of different salt adaptation strategies on the microbial diversity, activity, and settling of nitrifying sludge in sequencing batch reactors.

PubMed

Bassin, João Paulo; Kleerebezem, Robbert; Muyzer, Gerard; Rosado, Alexandre Soares; van Loosdrecht, Mark C M; Dezotti, Marcia

2012-02-01

The effect of salinity on the activity of nitrifying bacteria, floc characteristics, and microbial community structure accessed by fluorescent in situ hybridization and polymerase chain reaction-denaturing gradient gel electrophoresis techniques was investigated. Two sequencing batch reactors (SRB₁ and SBR₂) treating synthetic wastewater were subjected to increasing salt concentrations. In SBR₁, four salt concentrations (5, 10, 15, and 20 g NaCl/L) were tested, while in SBR₂, only two salt concentrations (10 and 20 g NaCl/L) were applied in a more shock-wise manner. The two different salt adaptation strategies caused different changes in microbial community structure, but did not change the nitrification performance, suggesting that regardless of the different nitrifying bacterial community present in the reactor, the nitrification process can be maintained stable within the salt range tested. Specific ammonium oxidation rates were more affected when salt increase was performed more rapidly and dropped 50% and 60% at 20 g NaCl/L for SBR₁ and SBR₂, respectively. A gradual increase in NaCl concentration had a positive effect on the settling properties (i.e., reduction of sludge volume index), although it caused a higher amount of suspended solids in the effluent. Higher organisms (e.g., protozoa, nematodes, and rotifers) as well as filamentous bacteria could not withstand the high salt concentrations.

Using Amplicon Sequencing To Characterize and Monitor Bacterial Diversity in Drinking Water Distribution Systems.

PubMed

Shaw, Jennifer L A; Monis, Paul; Weyrich, Laura S; Sawade, Emma; Drikas, Mary; Cooper, Alan J

2015-09-01

Drinking water assessments use a variety of microbial, physical, and chemical indicators to evaluate water treatment efficiency and product water quality. However, these indicators do not allow the complex biological communities, which can adversely impact the performance of drinking water distribution systems (DWDSs), to be characterized. Entire bacterial communities can be studied quickly and inexpensively using targeted metagenomic amplicon sequencing. Here, amplicon sequencing of the 16S rRNA gene region was performed alongside traditional water quality measures to assess the health, quality, and efficiency of two distinct, full-scale DWDSs: (i) a linear DWDS supplied with unfiltered water subjected to basic disinfection before distribution and (ii) a complex, branching DWDS treated by a four-stage water treatment plant (WTP) prior to disinfection and distribution. In both DWDSs bacterial communities differed significantly after disinfection, demonstrating the effectiveness of both treatment regimes. However, bacterial repopulation occurred further along in the DWDSs, and some end-user samples were more similar to the source water than to the postdisinfection water. Three sample locations appeared to be nitrified, displaying elevated nitrate levels and decreased ammonia levels, and nitrifying bacterial species, such as Nitrospira, were detected. Burkholderiales were abundant in samples containing large amounts of monochloramine, indicating resistance to disinfection. Genera known to contain pathogenic and fecal-associated species were also identified in several locations. From this study, we conclude that metagenomic amplicon sequencing is an informative method to support current compliance-based methods and can be used to reveal bacterial community interactions with the chemical and physical properties of DWDSs. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Biotransformation of acyclovir by an enriched nitrifying culture.

PubMed

Xu, Yifeng; Yuan, Zhiguo; Ni, Bing-Jie

2017-03-01

This work evaluates the biodegradation of the antiviral drug acyclovir by an enriched nitrifying culture during ammonia oxidation and without the addition of ammonium. The study on kinetics was accompanied with the structural elucidation of biotransformation products through batch biodegradation experiments at two different initial levels of acyclovir (15 mg L -1 and 15 μg L -1 ). The pseudo first order kinetic studies of acyclovir in the presence of ammonium indicated the higher degradation rates under higher ammonia oxidation rates than those constant degradation rates in the absence of ammonium. The positive correlation was found between acyclovir degradation rate and ammonia oxidation rate, confirming the cometabolism of acyclovir by the enriched nitrifying culture in the presence of ammonium. Formation of the product carboxy-acyclovir (P239) indicated the main biotransformation pathway was aerobic oxidation of the terminal hydroxyl group, which was independent on the metabolic type (i.e. cometabolism or metabolism). This enzyme-linked reaction might be catalyzed by monooxygenase from ammonia oxidizing bacteria or heterotrophs. The formation of carboxy-acyclovir was demonstrated to be irrelevant to the acyclovir concentrations applied, indicating the revealed biotransformation pathway might be the dominant removal pathway of acyclovir in wastewater treatment. Copyright © 2016 Elsevier Ltd. All rights reserved.

A zeta potential value determines the aggregate's size of penta-substituted [60]fullerene derivatives in aqueous suspension whereas positive charge is required for toxicity against bacterial cells.

PubMed

Deryabin, Dmitry G; Efremova, Ludmila V; Vasilchenko, Alexey S; Saidakova, Evgeniya V; Sizova, Elena A; Troshin, Pavel A; Zhilenkov, Alexander V; Khakina, Ekaterina A; Khakina, Ekaterina E

2015-08-08

The cause-effect relationships between physicochemical properties of amphiphilic [60]fullerene derivatives and their toxicity against bacterial cells have not yet been clarified. In this study, we report how the differences in the chemical structure of organic addends in 10 originally synthesized penta-substituted [60]fullerene derivatives modulate their zeta potential and aggregate's size in salt-free and salt-added aqueous suspensions as well as how these physicochemical characteristics affect the bioenergetics of freshwater Escherichia coli and marine Photobacterium phosphoreum bacteria. Dynamic light scattering, laser Doppler micro-electrophoresis, agarose gel electrophoresis, atomic force microscopy, and bioluminescence inhibition assay were used to characterize the fullerene aggregation behavior in aqueous solution and their interaction with the bacterial cell surface, following zeta potential changes and toxic effects. Dynamic light scattering results indicated the formation of self-assembled [60]fullerene aggregates in aqueous suspensions. The measurement of the zeta potential of the particles revealed that they have different surface charges. The relationship between these physicochemical characteristics was presented as an exponential regression that correctly described the dependence of the aggregate's size of penta-substituted [60]fullerene derivatives in salt-free aqueous suspension from zeta potential value. The prevalence of DLVO-related effects was shown in salt-added aqueous suspension that decreased zeta potential values and affected the aggregation of [60]fullerene derivatives expressed differently for individual compounds. A bioluminescence inhibition assay demonstrated that the toxic effect of [60]fullerene derivatives against E. coli cells was strictly determined by their positive zeta potential charge value being weakened against P. phosphoreum cells in an aquatic system of high salinity. Atomic force microscopy data suggested that the

A model for bacterial colonization of sinking aggregates.

PubMed

Bearon, R N

2007-01-01

Sinking aggregates provide important nutrient-rich environments for marine bacteria. Quantifying the rate at which motile bacteria colonize such aggregations is important in understanding the microbial loop in the pelagic food web. In this paper, a simple analytical model is presented to predict the rate at which bacteria undergoing a random walk encounter a sinking aggregate. The model incorporates the flow field generated by the sinking aggregate, the swimming behavior of the bacteria, and the interaction of the flow with the swimming behavior. An expression for the encounter rate is computed in the limit of large Péclet number when the random walk can be approximated by a diffusion process. Comparison with an individual-based numerical simulation is also given.

COMETABOLISM OF TRIHALOMETHANES BY NITRIFYING BIOFILTERS UNDER DRINKING WATER TREATMENT PLANT CONDITIONS

EPA Science Inventory

EPA Identifier: FP916412
Title: Cometabolism of Trihalomethanes by Nitrifying Biofilters Under Drinking Water Treatment Plant Conditions
Fellow (Principal Investigator): David G. Wahman
Institution: University of Texas at Austin
EPA ...

Transcriptional and physiological responses of nitrifying bacteria to heavy metal inhibition

EPA Science Inventory

Heavy metals have been shown to inhibit nitrification, a key process in the removal of nitrogen in wastewater treatment plants. In the present study, the effects of nickel, zinc, lead and cadmium on nitrifying enrichment cultures were studied in batch reactors. The transcriptiona...

Reaction rate constants and mean population percentage for nitrifiers in an alternating oxidation ditch system.

PubMed

Mantziaras, I D; Katsiri, A

2011-01-01

This paper presents a methodology for the determination of reaction rate constants for nitrifying bacteria and their mean population percentage in biomass in an alternating oxidation ditch system. The method used is based on the growth rate equations of the ASM1 model (IWA) (Henze et al. in Activated sludge models ASM1, ASM2, ASM2d, and ASM3. IWA Scientific and Technical Report no. 9, IWA Publishing, London, UK, 2000) and the application of mass balance equations for nitrifiers and ammonium nitrogen in an operational cycle of the ditch system. The system consists of two ditches operating in four phases. Data from a large-scale oxidation ditch pilot plant with a total volume of 120 m(3) within an experimental period of 8 months was used. Maximum specific growth rate for autotrophs (μ(A)) and the half-saturation constant for ammonium nitrogen (K(NH)) were found to be 0.36 day(-1) and 0.65 mgNH(4)-N/l, respectively. Additionally, the average population percentage of the nitrifiers in the biomass was estimated to be around 3%.

[Isolation of heterotrophic nitrifiers/aerobic denitrifiers and their roles in N2O production for different incubations].

PubMed

Jiang, Jing-Yan; Hu, Zheng-Hua; Huang, Yao

2009-07-15

Soil microorganisms are important sources of N2O for the atmosphere. Peak emissions of N2O are often observed after wetting of soil. The simultaneous heterotrophic nitrifying and aerobic denitrifying bacteria with respect to N2O emission were studied to obtain more information about the microbiologcal aspects of peak emissions. Using acetamide as the C and N source, two strains of nitrifying and denitrifying bacteria were isolated, coded as XM1 and HX2,respectively. XM1 strain was Gram-negative chain-like bacilli, and the HX2 was Gram-negative cocci. In enrichment culture, N2O production of HX2 was 76 times more than XM1. Two strains could grow with glucose, mannitol or sodium tartrate as sole carbon source, respectively. They could nitrify with sodium nitrate or denitrify with ammonium sulfate as unique nitrogen source, and produce intermediate product nitrite. XM1 strain growth velocity and nitrite formation were obviously higher than HX2. The phylogentic analysis based on partial 16S rDNA showed that two isolated strains were the closest relative of Pseudomonas sp.99% sequence similarity. Under different WFPS (water-filled-pore-space) conditions, the aerobic autoclaved soil incubation trial showed that, HX2 strain was suitable for growing in 30% WFPS, and N2O production was (36.01 +/- 2.48) ng/g which was 1.9 times than that in 60% WFPS. But XM1 was suitable for growing in 60% WFPS and almost had no N2O production. To investigate the nitrifying and denitrifying mechanisms of heterotrophic nitrifiers/aerobic denitrifiers should be useful for mastering the mitigation way of soil N2O emission in future.

Hydroxylamine diffusion can enhance N₂O emissions in nitrifying biofilms: a modeling study.

PubMed

Sabba, Fabrizio; Picioreanu, Cristian; Pérez, Julio; Nerenberg, Robert

2015-02-03

Wastewater treatment plants can be significant sources of nitrous oxide (N2O), a potent greenhouse gas. However, little is known about N2O emissions from biofilm processes. We adapted an existing suspended-growth mathematical model to explore N2O emissions from nitrifying biofilms. The model included N2O formation by ammonia-oxidizing bacteria (AOB) via the hydroxylamine and the nitrifier denitrification pathways. Our model suggested that N2O emissions from nitrifying biofilms could be significantly greater than from suspended growth systems under similar conditions. The main cause was the formation and diffusion of hydroxylamine, an AOB nitrification intermediate, from the aerobic to the anoxic regions of the biofilm. In the anoxic regions, hydroxylamine oxidation by AOB provided reducing equivalents used solely for nitrite reduction to N2O, since there was no competition with oxygen. For a continuous system, very high and very low dissolved oxygen (DO) concentrations resulted in lower emissions, while intermediate values led to higher emissions. Higher bulk ammonia concentrations and greater biofilm thicknesses increased emissions. The model effectively predicted N2O emissions from an actual pilot-scale granular sludge reactor for sidestream nitritation, but significantly underestimated the emissions when the NH2OH diffusion coefficient was assumed to be minimal. This numerical study suggests an unexpected and important role of hydroxylamine in N2O emission in biofilms.

Impacts of different N management regimes on nitrifier and denitrifier communities and N cycling in soil microenvironments

PubMed Central

Kong, Angela Y. Y.; Hristova, Krassimira; Scow, Kate M.; Six, Johan

2011-01-01

hypothesis was also not corroborated because canonical correspondence analyses revealed that AOB and denitrifier abundances were decoupled from potential gross N mineralization and nitrification rates and from inorganic N concentrations. Our third hypothesis was supported by the overall larger nitrifier, denitrifier, and total bacterial communities measured in the soil microaggregates compared to the cPOM and silt-and-clay. These results suggest that the microaggregates are microenvironments that preferentially stabilize C, and concomitantly promote the growth of nitrifier and denitrifier communities, thereby serving as potential hotspots for N2O losses. PMID:21339865

Bacterial diversity of soil aggregates of different sizes in various land use conditions

NASA Astrophysics Data System (ADS)

Ivanova, Ekaterina; Azida, Thakahova; Olga, Kutovaya

2014-05-01

The patterns of soil microbiome structure may be a universal and very sensitive indicator of soil quality (soil "health") used for optimization and biologization of agricultural systems. The understanding of how microbial diversity influenses, and is influenced by, the environment can only be attained by analyses at scales relevant to those at which processes influencing microbial diversity actually operate. The basic structural and functional unit of the soil is a soil aggregate, which is actually a microcosm of the associative co-existing groups of microorganisms that form characteristic ecological food chains. It is known that many important microbial processes occur in spatially segregated microenvironments in soil leading to a microscale biogeography. The Metagenomic library of typical chernozem in conditions of different land use systems was created. Total genomic DNA was extracted from 0.5 g of the frozen soil after mechanical destruction. Sample preparation and sequencing was performed on a GS Junior ("Roche»", Switzerland) according to manufacturer's recommendations, using the universal primers to the variable regions V4 gene 16S - rRNA - F515 (GTGCCAGCMGCCGCGGTAA) and R806 (GGACT-ACVSGGGTATCTAAT). It is shown that the system of land use is a stronger determinant of the taxonomic composition of the soil microbial community, rather than the size of the structural units. In soil samples from different land use systems the presence of accessory components was revealed. They may be used as indicators of processes of soil recovery, soil degradation or soil exhaustion processes occuring in the agroecosystems. The comparative analysis of microbial communities of chernozem aggregates investigated demonstrates the statistically valuable differences in the amount of bacterial phyla and Archean domain content as well as the species richness in aggregates of various size fractions. The occurrence of specific components in the taxonomic structure of micro-and macro-aggregates

Bioaugmentation of a biological contact oxidation ditch with indigenous nitrifying bacteria for in situ remediation of nitrogen-rich stream water.

PubMed

Jiao, Yan; Zhao, Qingliang; Jin, Wenbiao; Hao, Xiaodi; You, Shijie

2011-01-01

In this study, specialized bacteria were domesticated and cultivated with polluted stream water. The bioaugmentation of specialized bacteria would significantly enhance the removal efficiency of TN and NH4+-N from 25.9% to 50.3%, and from 34.5% to 60.1%, respectively. Concomitant increases in the number of microbial communities and the proportion of nitrifying bacteria were also identified by the most probable number (MPN) method. PCR-DGGE profiles revealed that the bacterial community could be successfully enriched and the ammonia-oxidizing bacteria communities were shown predominant by the species of Nitrosomonas. The biological contact oxidation ditch (BCOD) system augmented with specialized bacteria can be a viable alternative for treating polluted stream water to achieve improved nitrogen removal. Copyright © 2010 Elsevier Ltd. All rights reserved.

Ammonia oxidisers in a non-nitrifying Brazilian savanna soil.

PubMed

Catão, Elisa C P; Thion, Cécile; Krüger, R H; Prosser, James I

2017-11-01

Low nitrification rates in Brazilian savanna (Cerrado) soils have puzzled researchers for decades. Potential mechanisms include biological inhibitors, low pH, low microbial abundance and low soil moisture content, which hinders microbial activity, including ammonia oxidation. Two approaches were used to evaluate these potential mechanisms: (i) manipulation of soil moisture and pH in microcosms containing Cerrado soil and (ii) assessment of nitrification inhibition in slurries containing mixtures of Cerrado soil and an actively nitrifying agricultural soil. Despite high ammonium concentration in Cerrado soil microcosms, little NO3- accumulation was observed with increasing moisture or pH, but in some Cerrado soil slurries, ammonia-oxidising archaea (AOA) amoA transcripts were detected after 14 days. In mixed soil slurries, the final NO3- concentration reflected the initial proportions of agricultural and Cerrado soils in the mixture, providing no evidence of nitrification inhibitors in Cerrado soil. AOA community denaturing gradient gel electrophoresis profiles were similar in the mixed and nitrifying soils. These results suggest that nitrification in Cerrado soils is not constrained by water availability, ammonium availability, low pH or biological inhibitors, and alternative potential explanations for low nitrification levels are discussed. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Effects of recombinant protein misfolding and aggregation on bacterial membranes.

PubMed

Ami, D; Natalello, A; Schultz, T; Gatti-Lafranconi, P; Lotti, M; Doglia, S M; de Marco, A

2009-02-01

The expression of recombinant proteins is known to induce a metabolic rearrangement in the host cell. We used aggregation-sensitive model systems to study the effects elicited in Escherichia coli cells by the aggregation of recombinant glutathione-S-transferase and its fusion with the green fluorescent protein that, according to the expression conditions, accumulate intracellularly as soluble protein, or soluble and insoluble aggregates. We show that the folding state of the recombinant protein and the complexity of the intracellular aggregates critically affect the cell response. Specifically, protein misfolding and aggregation induce changes in specific host proteins involved in lipid metabolism and oxidative stress, a reduction in the membrane permeability, as well as a rearrangement of its lipid composition. The temporal evolution of the host cell response and that of the aggregation process pointed out that the misfolded protein and soluble aggregates are responsible for the membrane modifications and the changes in the host protein levels. Interestingly, native recombinant protein and large insoluble aggregates do not seem to activate stress markers and membrane rearrangements.

Protein aggregation in bacteria: the thin boundary between functionality and toxicity.

PubMed

Bednarska, Natalia G; Schymkowitz, Joost; Rousseau, Frederic; Van Eldere, Johan

2013-09-01

Misfolding and aggregation of proteins have a negative impact on all living organisms. In recent years, aggregation has been studied in detail due to its involvement in neurodegenerative diseases, including Alzheimer's, Parkinson's and Huntington's diseases, and type II diabetes--all associated with accumulation of amyloid fibrils. This research highlighted the central importance of protein homeostasis, or proteostasis for short, defined as the cellular state in which the proteome is both stable and functional. It implicates an equilibrium between synthesis, folding, trafficking, aggregation, disaggregation and degradation. In accordance with the eukaryotic systems, it has been documented that protein aggregation also reduces fitness of bacterial cells, but although our understanding of the cellular protein quality control systems is perhaps most detailed in bacteria, the use of bacterial proteostasis as a drug target remains little explored. Here we describe protein aggregation as a normal physiological process and its role in bacterial virulence and we shed light on how bacteria defend themselves against the toxic threat of aggregates. We review the impact of aggregates on bacterial viability and look at the ways that bacteria use to maintain a balance between aggregation and functionality. The proteostasis in bacteria can be interrupted via overexpression of proteins, certain antibiotics such as aminoglycosides, as well as antimicrobial peptides--all leading to loss of cell viability. Therefore intracellular protein aggregation and disruption of proteostatic balance in bacteria open up another strategy that should be explored towards the discovery of new antimicrobials.

Multiscale modeling of bacterial colonies: how pili mediate the dynamics of single cells and cellular aggregates

NASA Astrophysics Data System (ADS)

Pönisch, Wolfram; Weber, Christoph A.; Juckeland, Guido; Biais, Nicolas; Zaburdaev, Vasily

2017-01-01

Neisseria gonorrhoeae is the causative agent of one of the most common sexually transmitted diseases, gonorrhea. Over the past two decades there has been an alarming increase of reported gonorrhea cases where the bacteria were resistant to the most commonly used antibiotics thus prompting for alternative antimicrobial treatment strategies. The crucial step in this and many other bacterial infections is the formation of microcolonies, agglomerates consisting of up to several thousands of cells. The attachment and motility of cells on solid substrates as well as the cell-cell interactions are primarily mediated by type IV pili, long polymeric filaments protruding from the surface of cells. While the crucial role of pili in the assembly of microcolonies has been well recognized, the exact mechanisms of how they govern the formation and dynamics of microcolonies are still poorly understood. Here, we present a computational model of individual cells with explicit pili dynamics, force generation and pili-pili interactions. We employ the model to study a wide range of biological processes, such as the motility of individual cells on a surface, the heterogeneous cell motility within the large cell aggregates, and the merging dynamics and the self-assembly of microcolonies. The results of numerical simulations highlight the central role of pili generated forces in the formation of bacterial colonies and are in agreement with the available experimental observations. The model can quantify the behavior of multicellular bacterial colonies on biologically relevant temporal and spatial scales and can be easily adjusted to include the geometry and pili characteristics of various bacterial species. Ultimately, the combination of the microbiological experimental approach with the in silico model of bacterial colonies might provide new qualitative and quantitative insights on the development of bacterial infections and thus pave the way to new antimicrobial treatments.

Complete and simultaneous removal of ammonium and m-cresol in a nitrifying sequencing batch reactor.

PubMed

Zepeda, Alejandro; Ben-Youssef, Chérif; Rincón, Susana; Cuervo-López, Flor; Gómez, Jorge

2013-06-01

The kinetic behavior, oxidizing ability and tolerance to m-cresol of a nitrifying sludge exposed to different initial concentrations of m-cresol (0-150 mg C L(-1)) were evaluated in a sequencing batch reactor fed with 50 mg NH4 (+)-N L(-1) and operated during 4 months. Complete removal of ammonium and m-cresol was achieved independently of the initial concentration of aromatic compound in all the assays. Up to 25 mg m-cresol-C L(-1) (C/N ratio of 0.5), the nitrifying yield (Y-NO3 (-)) was 0.86 ± 0.05, indicating that the nitrate was the main product of the process; no biomass growth was detected. From 50 to 150 mg m-cresol-C L(-1) (1.0 ≤ C/N ≤ 3.0), simultaneous microbial growth and partial ammonium-to-nitrate conversion were obtained, reaching a maximum microbial total protein concentration of 0.763 g L(-1) (247 % of its initial value) and the lowest Y-NO3 (-) 0.53 ± 0.01 at 150 mg m-cresol-C L(-1). m-Cresol induced a significant decrease in the values of both specific rates of ammonium and nitrite oxidation, being the ammonium oxidation pathway the mainly inhibited. The nitrifying sludge was able to completely oxidize up to 150 mg m-cresol-C L(-1) by SBR cycle, reaching a maximum specific removal rate of 6.45 g m-cresol g(-1) microbial protein-N h(-1). The number of SBR cycles allowed a metabolic adaptation of the nitrifying consortium since nitrification inhibition decreased and faster oxidation of m-cresol took place throughout the cycles.

Effect of settled diatom‐aggregates on benthic nitrogen cycling

PubMed Central

Thamdrup, Bo; Stief, Peter; Glud, Ronnie N.

2017-01-01

Abstract The marine sediment hosts a mosaic of microhabitats. Recently it has been demonstrated that the settlement of phycodetrital aggregates can induce local changes in the benthic O2 distribution due to confined enrichment of organic material and alteration of the diffusional transport. Here, we show how this microscale O2 shift substantially affects benthic nitrogen cycling. In sediment incubations, the settlement of diatom‐aggregates markedly enhanced benthic O2 and NO3− consumption and stimulated NO2− and NH4+ production. Oxygen microprofiles revealed the rapid development of anoxic niches within and underneath the aggregates. During 120 h following the settling of the aggregates, denitrification of NO3− from the overlying water increased from 13.5 μmol m−2 h−1 to 24.3 μmol m−2 h−1, as quantified by 15N enrichment experiment. Simultaneously, N2 production from coupled nitrification‐denitrification decreased from 33.4 μmol m−2 h−1 to 25.9 μmol m−2 h−1, probably due to temporary inhibition of the benthic nitrifying community. The two effects were of similar magnitude and left the total N2 production almost unaltered. At the aggregate surface, nitrification was, conversely, very efficient in oxidizing NH4+ liberated by mineralization of the aggregates. The produced NO3− was preferentially released into the overlying water and only a minor fraction contributed to denitrification activity. Overall, our data indicate that the abrupt change in O2 microdistribution caused by aggregates stimulates denitrification of NO3− from the overlying water, and loosens the coupling between benthic nitrification and denitrification both in time and space. The study contributes to expanding the conceptual and quantitative understanding of how nitrogen cycling is regulated in dynamic benthic environments. PMID:29456269

Dynamics of nitrifying bacterial communities in the Seine river and estuary as affected by changes in the treatment of Paris wastewater : a comparison of 2001-2003 vs 2012-2013 periods

NASA Astrophysics Data System (ADS)

Aissa Grouz, Najla; Billen, Gilles; Garnier, Josette; Mercier, Benjamin; Martinez, Anun

2014-05-01

The major branch of the Seine river from the confluence with the Marne river to the entrance of the estuary is deeply affected by the release of wastewater from the huge Paris agglomeration. In the first years of 2000, the largest part of the effluents were still discharged at the Seine-Aval (Achères) treatment plant with only a standard, low residence time, activated sludge treatment, thus releasing a high ammonium load. NH4 concentration as high as 7 mgN/l were frequently observed downstream from Paris agglomeration. Cébron et al. (2003, 2005) and Garnier et al. 2007 described in details how this massive reduced nitrogen concentrations triggered the growth of nitrifying bacteria, already present in the upstream Seine and Marne rivers, but also brought in large amount by the effluents of the wastewater treatment plant themselves. The decrease of ammonium concentration was slow, however, and was only completed 200 km downstream, in the upper estuarine area, where it causes a severe oxygen deficiency. Since 2007, important changes occurred in the treatment of nitrogen in the Parisian wastewater purification plants. In 2007, the Seine-Aval plant treated up to 90% of the ammonium contained in wastewater through nitrification, and 30% of the total supply of nitrates is treated by denitrification. These modifications have of course favorably affected the water quality of the Seine river: ammonium concentrations are reduced by a factor of 5 and the area of oxygen depletion in the upstream estuary is no more observed. However, nitrites, still released in the effluents, are a matter of concern for the water quality of the Seine downstream from Paris. Using measurements of potential microbial activities carried out with the same experimental protocol for the 2000-2003 and 2012-2013 periods, we here examine and model the dynamics of ammonium oxidizing and nitrite oxidizing microbial populations before and after the implementation of nitrification treatment of Paris

Respirometric response and microbial succession of nitrifying sludge to m-cresol pulses in a sequencing batch reactor.

PubMed

Ordaz, Alberto; Sánchez, Mariana; Rivera, Rodrigo; Rojas, Rafael; Zepeda, Alejandro

2017-02-01

A nitrifying consortium was kinetically, stoichiometrically and molecularly characterized via the in situ pulse respirometric method and pyrosequencing analysis before and after the addition of m-cresol (25 mg C L -1 ) in a sequencing batch reactor (SBR). Five important kinetic and stoichiometric parameters were determined: the maximum oxygen uptake rate, the maximum nitrification rate, the oxidation yield, the biomass growth yield, and the substrate affinity constant. An inhibitory effect was observed in the nitrification process with a recovery of this by up to eight SBR cycles after m-cresol was added to the system. However, full recovery of the nitrification process was not observed, as the maximum oxygen uptake rate was 25% lower than that of the previous operation without m-cresol addition. Furthermore, the pyrosequencing analyses of the nitrifying consortium after the addition of only two pulses of 25 mg C L -1 m-cresol showed an important microbial community change represented by a decrease in the nitrifying populations and an increase in the populations degrading phenolic compounds.

Role of Multicellular Aggregates in Biofilm Formation

PubMed Central

Kragh, Kasper N.; Hutchison, Jaime B.; Melaugh, Gavin; Rodesney, Chris; Roberts, Aled E. L.; Irie, Yasuhiko; Jensen, Peter Ø.; Diggle, Stephen P.; Allen, Rosalind J.

2016-01-01

ABSTRACT In traditional models of in vitro biofilm development, individual bacterial cells seed a surface, multiply, and mature into multicellular, three-dimensional structures. Much research has been devoted to elucidating the mechanisms governing the initial attachment of single cells to surfaces. However, in natural environments and during infection, bacterial cells tend to clump as multicellular aggregates, and biofilms can also slough off aggregates as a part of the dispersal process. This makes it likely that biofilms are often seeded by aggregates and single cells, yet how these aggregates impact biofilm initiation and development is not known. Here we use a combination of experimental and computational approaches to determine the relative fitness of single cells and preformed aggregates during early development of Pseudomonas aeruginosa biofilms. We find that the relative fitness of aggregates depends markedly on the density of surrounding single cells, i.e., the level of competition for growth resources. When competition between aggregates and single cells is low, an aggregate has a growth disadvantage because the aggregate interior has poor access to growth resources. However, if competition is high, aggregates exhibit higher fitness, because extending vertically above the surface gives cells at the top of aggregates better access to growth resources. Other advantages of seeding by aggregates, such as earlier switching to a biofilm-like phenotype and enhanced resilience toward antibiotics and immune response, may add to this ecological benefit. Our findings suggest that current models of biofilm formation should be reconsidered to incorporate the role of aggregates in biofilm initiation. PMID:27006463

A robust nitrifying community in a bioreactor at 50 °C opens up the path for thermophilic nitrogen removal.

PubMed

Courtens, Emilie Np; Spieck, Eva; Vilchez-Vargas, Ramiro; Bodé, Samuel; Boeckx, Pascal; Schouten, Stefan; Jauregui, Ruy; Pieper, Dietmar H; Vlaeminck, Siegfried E; Boon, Nico

2016-09-01

The increasing production of nitrogen-containing fertilizers is crucial to meet the global food demand, yet high losses of reactive nitrogen associated with the food production/consumption chain progressively deteriorate the natural environment. Currently, mesophilic nitrogen-removing microbes eliminate nitrogen from wastewaters. Although thermophilic nitrifiers have been separately enriched from natural environments, no bioreactors are described that couple these processes for the treatment of nitrogen in hot wastewaters. Samples from composting facilities were used as inoculum for the batch-wise enrichment of thermophilic nitrifiers (350 days). Subsequently, the enrichments were transferred to a bioreactor to obtain a stable, high-rate nitrifying process (560 days). The community contained up to 17% ammonia-oxidizing archaea (AOAs) closely related to 'Candidatus Nitrososphaera gargensis', and 25% nitrite-oxidizing bacteria (NOBs) related to Nitrospira calida. Incorporation of (13)C-derived bicarbonate into the respective characteristic membrane lipids during nitrification supported their activity as autotrophs. Specific activities up to 198±10 and 894±81 mg N g(-1) VSS per day for AOAs and NOBs were measured, where NOBs were 33% more sensitive to free ammonia. The NOBs were extremely sensitive to free nitrous acid, whereas the AOAs could only be inhibited by high nitrite concentrations, independent of the free nitrous acid concentration. The observed difference in product/substrate inhibition could facilitate the development of NOB inhibition strategies to achieve more cost-effective processes such as deammonification. This study describes the enrichment of autotrophic thermophilic nitrifiers from a nutrient-rich environment and the successful operation of a thermophilic nitrifying bioreactor for the first time, facilitating opportunities for thermophilic nitrogen removal biotechnology.

A robust nitrifying community in a bioreactor at 50 °C opens up the path for thermophilic nitrogen removal

PubMed Central

Courtens, Emilie NP; Spieck, Eva; Vilchez-Vargas, Ramiro; Bodé, Samuel; Boeckx, Pascal; Schouten, Stefan; Jauregui, Ruy; Pieper, Dietmar H; Vlaeminck, Siegfried E; Boon, Nico

2016-01-01

The increasing production of nitrogen-containing fertilizers is crucial to meet the global food demand, yet high losses of reactive nitrogen associated with the food production/consumption chain progressively deteriorate the natural environment. Currently, mesophilic nitrogen-removing microbes eliminate nitrogen from wastewaters. Although thermophilic nitrifiers have been separately enriched from natural environments, no bioreactors are described that couple these processes for the treatment of nitrogen in hot wastewaters. Samples from composting facilities were used as inoculum for the batch-wise enrichment of thermophilic nitrifiers (350 days). Subsequently, the enrichments were transferred to a bioreactor to obtain a stable, high-rate nitrifying process (560 days). The community contained up to 17% ammonia-oxidizing archaea (AOAs) closely related to ‘Candidatus Nitrososphaera gargensis', and 25% nitrite-oxidizing bacteria (NOBs) related to Nitrospira calida. Incorporation of 13C-derived bicarbonate into the respective characteristic membrane lipids during nitrification supported their activity as autotrophs. Specific activities up to 198±10 and 894±81 mg N g−1 VSS per day for AOAs and NOBs were measured, where NOBs were 33% more sensitive to free ammonia. The NOBs were extremely sensitive to free nitrous acid, whereas the AOAs could only be inhibited by high nitrite concentrations, independent of the free nitrous acid concentration. The observed difference in product/substrate inhibition could facilitate the development of NOB inhibition strategies to achieve more cost-effective processes such as deammonification. This study describes the enrichment of autotrophic thermophilic nitrifiers from a nutrient-rich environment and the successful operation of a thermophilic nitrifying bioreactor for the first time, facilitating opportunities for thermophilic nitrogen removal biotechnology. PMID:26894446

Active motility in bimodular bacterial aggregates

NASA Astrophysics Data System (ADS)

Zeng, Yu; Liu, Bin

2017-11-01

Dispersal capability is essential for microorganisms to achieve long-distance translocation, thus crucial for their abundance in various environments. In general, active dispersals are attributed to the movements of self-powered planktonic cells, while sessile cells that live a colonial life often disperse passively through flow entrainments. Here, we report another means of active dispersal employed by aggregates of sessile cells. The spherical rosette colonies of the bacterium Caulobacter crescentus are aggregates of sessile stalked cells, of which a small proportion undergo cell division, grow active flagella and effect whole-rosette motility. We show that these rosettes actively disperse both in bulk water and near the solid-liquid interface. In particular, the proximity of a self-powered rosette to the solid surface promotes a rolling movement, leading to its persistent transportation along the solid boundary. The active dispersal of these rosettes demonstrated a novel mode of colonial transportation that is based on the division of labor between sessile and motile cells. The authors thank the support of National Science Foundation CREST: Center for Cellular and Biomolecular Machines at UC Merced (NSF-HRD-1547848).

Hydrodynamic characteristics of airlift nitrifying reactor using carrier-induced granular sludge.

PubMed

Jin, Ren-Cun; Zheng, Ping; Mahmood, Qaisar; Zhang, Lei

2008-09-15

Since nitrification is the rate-limiting step in the biological nitrogen removal from wastewater, many studies have been conducted on the immobilization of nitrifying bacteria. A laboratory-scale investigation was carried out to scrutinize the effectiveness of activated carbon carrier addition for granulation of nitrifying sludge in a continuous-flow airlift bioreactor and to study the hydrodynamics of the reactor with carrier-induced granules. The results showed that the granular sludge began to appear and matured 60 and 108 days, respectively, after addition of carriers, while no granule was observed in the absence of carriers in the control test. The mature granules had a diameter of 0.5-5 mm (1.6 mm in average), settling velocity 22.3-55.8 m h(-1) and specific gravity of 1.086. The relationship between the two important hydrodynamic coefficients, i.e. gas holdup and liquid circulation velocity, and the superficial gas velocity were established by a simple model and were confirmed experimentally. The model also could predict the critical superficial gas velocity for liquid circulation and that for granules circulation, with respective values of 1.017 and 2.662 cm min(-1), accurately.

Impact of seasonal changes in nutrient loading on distribution and activity of nitrifiers in a tropical estuary

NASA Astrophysics Data System (ADS)

Vipindas, P. V.; Anas, Abdulaziz; Jayalakshmy, K. V.; Lallu, K. R.; Benny, P. Y.; Shanta, Nair

2018-02-01

Estuaries are ecologically important environments, which function as the reception point of nitrogenous inputs of terrestrial and anthropogenic origin. In the present study, we discuss the influence of nutrient characteristics on the distribution and activity of nitrifiers in the water column of Cochin Estuary (CE), a tropical estuary along the southeast Arabian Sea (SEAS). Nitrifying bacteria (i.e. Ammonia- (AOB) and nitrite- (NOB) -oxidizing bacteria), which were enumerated using fluorescent in situ hybridization (FISH), showed marked seasonality while maintaining the abundance within an order of 107 cells L-1. Denaturing Gradient Gel Electrophoresis (DGGE) analysis of AOB exhibited spatio-temporal adaptability without much variation. Nitrification rate in the CE ranged from 2.25 to 426.17 nmol N L-1 h-1 and it was 10-40 fold higher during the pre-monsoon compared with the monsoon. We attributed this increase to high nutrient availability during pre-monsoon due to low flushing rate of the estuary. The study shows that the distribution and activities of nitrifiers in the CE are modulated by the changes in nutrient concentration imparted by the monsoon-driven seasonal variation in river-water discharge and flushing.

Nitrification treatment of swine wastewater with acclimated nitrifying sludge immobilized in polymer pellets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vanotti, M.B.; Hunt, P.G.

2000-04-01

Nitrification of ammonia (NH{sub 4}{sup +}) is a critical component for improved systems of animal wastewater treatment. One of the most effective processes uses nitrifying microorganisms encapsulated in polymer resins. It is used in Japan in municipal wastewater treatment plants for higher nitrification rates, shorter hydraulic retention times (HRT), and lower aeration treatment cost. The authors evaluated whether this technology could be adapted for treatment of higher-strength lagoon swine wastewaters containing {approximately}230 mg NH{sub 4}-N/L and 195 mg BOD{sub 5}/L. A culture of acclimated lagoon nitrifying sludge (ALNS) was prepared from a nitrifying biofilm developed in an overland flow soilmore » using fill-and-draw cultivation. The ALNS was successfully immobilized in 3- to 5-mm polyvinyl alcohol (PVA) polymer pellets by a PVA-freezing method. Swine wastewater was treated in aerated, suspended bioreactors with a 15% (w/v) pellet concentration using batch and continuous flow treatment. Alkalinity was supplemented with inorganic carbon to maintain the liquid pH within an optimum range (7.7--8.4). In batch treatment, only 14 h were needed for nitrification of NH{sub 4}{sup +}. Ammonia was nitrified readily, decreasing at a rate of 16.1 mg NH{sub 4}-N/L h. In contrast, it took 10 d for a control (no-pellets) aerated reactor to start nitrification; furthermore, 70% of the N was lost by air stripping. Without alkalinity supplements, the pH of the liquid fell to 6.0--6.2, and NH{sub 4}{sup +} oxidation stopped. In continuous flow treatment, nitrification efficiencies of 95% were obtained with NH{sub 4}{sup +} loading rates of 418 mg-N/L-reactor d (2.73 g-N/g-pellet d) and an HRT of 12 h. The rate of nitrification obtained with HRT of 4 h was 567 mg-N/L d. In all cases, the NH{sub 4}-N removed was entirely recovered in oxidized N forms. Nitrification rates obtained in this work were not greatly affected by high NH{sub 4}{sup +} or BOD concentration of swine

Ralstonia insidiosa induces cell aggregation by Listeria monocytogenes

USDA-ARS?s Scientific Manuscript database

Biofilm formation is an important strategy for foodborne bacterial pathogens to survive in stressful environments such as fresh produce processing facilities. Bacterial cell aggregation strongly promotes the initiation of microcolonies and the formation of biofilms on abiological surfaces. We previ...

Links among nitrification, nitrifier communities, and edaphic properties in contrasting soils receiving dairy slurry.

PubMed

Fortuna, Ann-Marie; Honeycutt, C Wayne; Vandemark, George; Griffin, Timothy S; Larkin, Robert P; He, Zhongqi; Wienhold, Brian J; Sistani, Karamat R; Albrecht, Stephan L; Woodbury, Bryan L; Torbert, Henry A; Powell, J Mark; Hubbard, Robert K; Eigenberg, Roger A; Wright, Robert J; Alldredge, J Richard; Harsh, James B

2012-01-01

Soil biotic and abiotic factors strongly influence nitrogen (N) availability and increases in nitrification rates associated with the application of manure. In this study, we examine the effects of edaphic properties and a dairy (Bos taurus) slurry amendment on N availability, nitrification rates and nitrifier communities. Soils of variable texture and clay mineralogy were collected from six USDA-ARS research sites and incubated for 28 d with and without dairy slurry applied at a rate of ~300 kg N ha(-1). Periodically, subsamples were removed for analyses of 2 M KCl extractable N and nitrification potential, as well as gene copy numbers of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Spearman coefficients for nitrification potentials and AOB copy number were positively correlated with total soil C, total soil N, cation exchange capacity, and clay mineralogy in treatments with and without slurry application. Our data show that the quantity and type of clay minerals present in a soil affect nitrifier populations, nitrification rates, and the release of inorganic N. Nitrogen mineralization, nitrification potentials, and edaphic properties were positively correlated with AOB gene copy numbers. On average, AOA gene copy numbers were an order of magnitude lower than those of AOB across the six soils and did not increase with slurry application. Our research suggests that the two nitrifier communities overlap but have different optimum environmental conditions for growth and activity that are partly determined by the interaction of manure-derived ammonium with soil properties. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle

PubMed Central

Kits, K. Dimitri; Sedlacek, Christopher J.; Lebedeva, Elena V.; Han, Ping; Bulaev, Alexandr; Pjevac, Petra; Daebeler, Anne; Romano, Stefano; Albertsen, Mads; Stein, Lisa Y.; Daims, Holger; Wagner, Michael

2017-01-01

Summary paragraph Nitrification, the oxidation of ammonia (NH3) via nitrite (NO2-) to nitrate (NO3-), is a key process of the biogeochemical nitrogen cycle. For decades, ammonia and nitrite oxidation were thought to be separately catalyzed by ammonia-oxidizing bacteria (AOB) and archaea (AOA), and by nitrite-oxidizing bacteria (NOB). The recent discovery of complete ammonia oxidizers (comammox) in the NOB genus Nitrospira1,2, which alone convert ammonia to nitrate, raised questions about the ecological niches where comammox Nitrospira successfully compete with canonical nitrifiers. Here we isolated the first pure culture of a comammox bacterium, Nitrospira inopinata, and show that it is adapted to slow growth in oligotrophic and dynamic habitats based on a high affinity for ammonia, low maximum rate of ammonia oxidation, high growth yield compared to canonical nitrifiers, and genomic potential for alternative metabolisms. The nitrification kinetics of four AOA from soil and hot springs were determined for comparison. Their surprisingly poor substrate affinities and lower growth yields reveal that, in contrast to earlier assumptions, not all AOA are most competitive in strongly oligotrophic environments and that N. inopinata has the highest substrate affinity of all analyzed ammonia oxidizer isolates except the marine AOA Nitrosopumilus maritimus SCM13. These results suggest a role of comammox organisms for nitrification under oligotrophic and dynamic conditions. PMID:28847001

Nitrogen-removal performance and community structure of nitrifying bacteria under different aeration modes in an oxidation ditch.

PubMed

Guo, Chang-Zi; Fu, Wei; Chen, Xue-Mei; Peng, Dang-Cong; Jin, Peng-Kang

2013-07-01

Oxidation-ditch operation modes were simulated using sequencing batch reactors (SBRs) with alternate stirring and aerating. The nitrogen-removal efficiencies and nitrifying characteristics of two aeration modes, point aeration and step aeration, were investigated. Under the same air-supply capacity, oxygen dissolved more efficiently in the system with point aeration, forming a larger aerobic zone. The nitrifying effects were similar in point aeration and step aeration, where the average removal efficiencies of NH4(+) N were 98% and 96%, respectively. When the proportion of anoxic and oxic zones was 1, the average removal efficiencies of total nitrogen (TN) were 45% and 66% under point aeration and step aeration, respectively. Step aeration was more beneficial to both anoxic denitrification and simultaneous nitrification and denitrification (SND). The maximum specific ammonia-uptake rates (AUR) of point aeration and step aeration were 4.7 and 4.9 mg NH4(+)/(gMLVSS h), respectively, while the maximum specific nitrite-uptake rates (NUR) of the two systems were 7.4 and 5.3 mg NO2(-)-N/(gMLVSS h), respectively. The proportions of ammonia-oxidizing bacteria (AOB) to all bacteria were 5.1% under point aeration and 7.0% under step aeration, and the proportions of nitrite-oxidizing bacteria (NOB) reached 6.5% and 9.0% under point and step aeration, respectively. The dominant genera of AOB and NOB were Nitrosococcus and Nitrospira, which accounted for 90% and 91%, respectively, under point aeration, and the diversity of nitrifying bacteria was lower than under step aeration. Point aeration was selective of nitrifying bacteria. The abundance of NOB was greater than that of AOB in both of the operation modes, and complete transformation of NH4(+) N to NO3(-)-N was observed without NO2(-)-N accumulation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Physical soil architectural traits are functionally linked to carbon decomposition and bacterial diversity.

PubMed

Rabbi, S M F; Daniel, H; Lockwood, P V; Macdonald, C; Pereg, L; Tighe, M; Wilson, B R; Young, I M

2016-09-12

Aggregates play a key role in protecting soil organic carbon (SOC) from microbial decomposition. The objectives of this study were to investigate the influence of pore geometry on the organic carbon decomposition rate and bacterial diversity in both macro- (250-2000 μm) and micro-aggregates (53-250 μm) using field samples. Four sites of contrasting land use on Alfisols (i.e. native pasture, crop/pasture rotation, woodland) were investigated. 3D Pore geometry of the micro-aggregates and macro-aggregates were examined by X-ray computed tomography (μCT). The occluded particulate organic carbon (oPOC) of aggregates was measured by size and density fractionation methods. Micro-aggregates had 54% less μCT observed porosity but 64% more oPOC compared with macro-aggregates. In addition, the pore connectivity in micro-aggregates was lower than macro-aggregates. Despite both lower μCT observed porosity and pore connectivity in micro-aggregates, the organic carbon decomposition rate constant (Ksoc) was similar in both aggregate size ranges. Structural equation modelling showed a strong positive relationship of the concentration of oPOC with bacterial diversity in aggregates. We use these findings to propose a conceptual model that illustrates the dynamic links between substrate, bacterial diversity, and pore geometry that suggests a structural explanation for differences in bacterial diversity across aggregate sizes.

Physical soil architectural traits are functionally linked to carbon decomposition and bacterial diversity

PubMed Central

Rabbi, S. M. F.; Daniel, H.; Lockwood, P. V.; Macdonald, C.; Pereg, L.; Tighe, M.; Wilson, B. R.; Young, I. M.

2016-01-01

Aggregates play a key role in protecting soil organic carbon (SOC) from microbial decomposition. The objectives of this study were to investigate the influence of pore geometry on the organic carbon decomposition rate and bacterial diversity in both macro- (250–2000 μm) and micro-aggregates (53–250 μm) using field samples. Four sites of contrasting land use on Alfisols (i.e. native pasture, crop/pasture rotation, woodland) were investigated. 3D Pore geometry of the micro-aggregates and macro-aggregates were examined by X-ray computed tomography (μCT). The occluded particulate organic carbon (oPOC) of aggregates was measured by size and density fractionation methods. Micro-aggregates had 54% less μCT observed porosity but 64% more oPOC compared with macro-aggregates. In addition, the pore connectivity in micro-aggregates was lower than macro-aggregates. Despite both lower μCT observed porosity and pore connectivity in micro-aggregates, the organic carbon decomposition rate constant (Ksoc) was similar in both aggregate size ranges. Structural equation modelling showed a strong positive relationship of the concentration of oPOC with bacterial diversity in aggregates. We use these findings to propose a conceptual model that illustrates the dynamic links between substrate, bacterial diversity, and pore geometry that suggests a structural explanation for differences in bacterial diversity across aggregate sizes. PMID:27615807

Two-step nitrification in a pure moving bed biofilm reactor-membrane bioreactor for wastewater treatment: nitrifying and denitrifying microbial populations and kinetic modeling.

PubMed

Leyva-Díaz, J C; González-Martínez, A; Muñío, M M; Poyatos, J M

2015-12-01

The moving bed biofilm reactor-membrane bioreactor (MBBR-MBR) is a novel solution to conventional activated sludge processes and membrane bioreactors. In this study, a pure MBBR-MBR was studied. The pure MBBR-MBR mainly had attached biomass. The bioreactor operated with a hydraulic retention time (HRT) of 9.5 h. The kinetic parameters for heterotrophic and autotrophic biomasses, mainly nitrite-oxidizing bacteria (NOB), were evaluated. The analysis of the bacterial community structure of the ammonium-oxidizing bacteria (AOB), NOB, and denitrifying bacteria (DeNB) from the pure MBBR-MBR was carried out by means of pyrosequencing to detect and quantify the contribution of the nitrifying and denitrifying bacteria in the total bacterial community. The relative abundance of AOB, NOB, and DeNB were 5, 1, and 3%, respectively, in the mixed liquor suspended solids (MLSS), and these percentages were 18, 5, and 2%, respectively, in the biofilm density (BD) attached to carriers. The pure MBBR-MBR had a high efficiency of total nitrogen (TN) removal of 71.81±16.04%, which could reside in the different bacterial assemblages in the fixed biofilm on the carriers. In this regard, the kinetic parameters for autotrophic biomass had values of YA=2.3465 mg O2 mg N(-1), μm, A=0.7169 h(-1), and KNH=2.0748 mg NL(-1).

Soil C and N statuses determine the effect of maize inoculation by plant growth-promoting rhizobacteria on nitrifying and denitrifying communities.

PubMed

Florio, Alessandro; Pommier, Thomas; Gervaix, Jonathan; Bérard, Annette; Le Roux, Xavier

2017-08-21

Maize inoculation by Azospirillum stimulates root growth, along with soil nitrogen (N) uptake and root carbon (C) exudation, thus increasing N use efficiency. However, inoculation effects on soil N-cycling microbial communities have been overlooked. We hypothesized that inoculation would (i) increase roots-nitrifiers competition for ammonium, and thus decrease nitrifier abundance; and (ii) increase roots-denitrifiers competition for nitrate and C supply to denitrifiers by root exudation, and thus limit or benefit denitrifiers depending on the resource (N or C) mostly limiting these microorganisms. We quantified (de)nitrifiers abundance and activity in the rhizosphere of inoculated and non-inoculated maize on 4 sites over 2 years, and ancillary soil variables. Inoculation effects on nitrification and nitrifiers (AOA, AOB) were not consistent between the three sampling dates. Inoculation influenced denitrifiers abundance (nirK, nirS) differently among sites. In sites with high C limitation for denitrifiers (i.e. limitation of denitrification by C > 66%), inoculation increased nirS-denitrifier abundance (up to 56%) and gross N 2 O production (up to 84%), likely due to increased root C exudation. Conversely, in sites with low C limitation (<47%), inoculation decreased nirS-denitrifier abundance (down to -23%) and gross N 2 O production (down to -18%) likely due to an increased roots-denitrifiers competition for nitrate.

Challenges for simultaneous nitrification, denitrification, and phosphorus removal in microbial aggregates: mass transfer limitation and nitrous oxide production.

PubMed

Meyer, Rikke Louise; Zeng, Raymond Jianxiong; Giugliano, Valerio; Blackall, Linda Louise

2005-05-01

The microbial community composition and activity was investigated in aggregates from a lab-scale bioreactor, in which nitrification, denitrification and phosphorus removal occurred simultaneously. The biomass was highly enriched for polyphosphate accumulating organisms facilitating complete removal of phosphorus from the bulk liquid; however, some inorganic nitrogen still remained at the end of the reactor cycle. This was ascribed to incomplete coupling of nitrification and denitrification causing NO(3)(-) accumulation. After 2 h of aeration, denitrification was dependent on the activity of nitrifying bacteria facilitating the formation of anoxic zones in the aggregates; hence, denitrification could not occur without simultaneous nitrification towards the end of the reactor cycle. Nitrous oxide was identified as a product of denitrification, when based on stored PHA as carbon source. This observation is of critical importance to the outlook of applying PHA-driven denitrification in activated sludge processes.

Autotrophic growth of nitrifying community in an agricultural soil

PubMed Central

Xia, Weiwei; Zhang, Caixia; Zeng, Xiaowei; Feng, Youzhi; Weng, Jiahua; Lin, Xiangui; Zhu, Jianguo; Xiong, Zhengqin; Xu, Jian; Cai, Zucong; Jia, Zhongjun

2011-01-01

The two-step nitrification process is an integral part of the global nitrogen cycle, and it is accomplished by distinctly different nitrifiers. By combining DNA-based stable isotope probing (SIP) and high-throughput pyrosequencing, we present the molecular evidence for autotrophic growth of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in agricultural soil upon ammonium fertilization. Time-course incubation of SIP microcosms indicated that the amoA genes of AOB was increasingly labeled by 13CO2 after incubation for 3, 7 and 28 days during active nitrification, whereas labeling of the AOA amoA gene was detected to a much lesser extent only after a 28-day incubation. Phylogenetic analysis of the 13C-labeled amoA and 16S rRNA genes revealed that the Nitrosospira cluster 3-like sequences dominate the active AOB community and that active AOA is affiliated with the moderately thermophilic Nitrososphaera gargensis from a hot spring. The higher relative frequency of Nitrospira-like NOB in the 13C-labeled DNA suggests that it may be more actively involved in nitrite oxidation than Nitrobacter-like NOB. Furthermore, the acetylene inhibition technique showed that 13CO2 assimilation by AOB, AOA and NOB occurs only when ammonia oxidation is not blocked, which provides strong hints for the chemolithoautotrophy of nitrifying community in complex soil environments. These results show that the microbial community of AOB and NOB dominates the nitrification process in the agricultural soil tested. PMID:21326337

Identification of key nitrous oxide production pathways in aerobic partial nitrifying granules.

PubMed

Ishii, Satoshi; Song, Yanjun; Rathnayake, Lashitha; Tumendelger, Azzaya; Satoh, Hisashi; Toyoda, Sakae; Yoshida, Naohiro; Okabe, Satoshi

2014-10-01

The identification of the key nitrous oxide (N2O) production pathways is important to establish a strategy to mitigate N2O emission. In this study, we combined real-time gas-monitoring analysis, (15)N stable isotope analysis, denitrification functional gene transcriptome analysis and microscale N2O concentration measurements to identify the main N2O producers in a partial nitrification (PN) aerobic granule reactor, which was fed with ammonium and acetate. Our results suggest that heterotrophic denitrification was the main contributor to N2O production in our PN aerobic granule reactor. The heterotrophic denitrifiers were probably related to Rhodocyclales bacteria, although different types of bacteria were active in the initial and latter stages of the PN reaction cycles, most likely in response to the presence of acetate. Hydroxylamine oxidation and nitrifier denitrification occurred, but their contribution to N2O emission was relatively small (20-30%) compared with heterotrophic denitrification. Our approach can be useful to quantitatively examine the relative contributions of the three pathways (hydroxylamine oxidation, nitrifier denitrification and heterotrophic denitrification) to N2O emission in mixed microbial populations. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Evidence of soluble microbial products accelerating chloramine decay in nitrifying bulk water samples.

PubMed

Bal Krishna, K C; Sathasivan, Arumugam; Chandra Sarker, Dipok

2012-09-01

The discovery of a microbially derived soluble product that accelerates chloramine decay is described. Nitrifying bacteria are believed to be wholly responsible for rapid chloramine loss in drinking water systems. However, a recent investigation showed that an unidentified soluble agent significantly accelerated chloramine decay. The agent was suspected to be either natural organic matter (NOM) or soluble microbial products (SMPs). A laboratory scale reactor was fed chloraminated reverse osmosis (RO) treated water to eliminate the interference from NOM. Once nitrification had set in, experiments were conducted on the reactor and feed waters to determine the identity of the component. The study showed the presence of SMPs released by microbes in severely nitrified waters. Further experiments proved that the SMPs significantly accelerated chloramine decay, probably through catalytic reaction. Moreover, application of common protein denaturing techniques stopped the reaction implying that the compound responsible was likely to be a protein. This significant finding will pave the way for better control of chloramine in the distribution systems. Copyright © 2012 Elsevier Ltd. All rights reserved.

Diatom-associated bacteria are required for aggregation of Thalassiosira weissflogii

PubMed Central

Gärdes, Astrid; Iversen, Morten H; Grossart, Hans-Peter; Passow, Uta; Ullrich, Matthias S

2011-01-01

Aggregation of algae, mainly diatoms, is an important process in marine systems leading to the settling of particulate organic carbon predominantly in the form of marine snow. Exudation products of phytoplankton form transparent exopolymer particles (TEP), which acts as the glue for particle aggregation. Heterotrophic bacteria interacting with phytoplankton may influence TEP formation and phytoplankton aggregation. This bacterial impact has not been explored in detail. We hypothesized that bacteria attaching to Thalassiosira weissflogii might interact in a yet-to-be determined manner, which could impact TEP formation and aggregate abundance. The role of individual T. weissflogii-attaching and free-living new bacterial isolates for TEP production and diatom aggregation was investigated in vitro. T. weissflogii did not aggregate in axenic culture, and striking differences in aggregation dynamics and TEP abundance were observed when diatom cultures were inoculated with either diatom-attaching or free-living bacteria. The data indicated that free-living bacteria might not influence aggregation whereas bacteria attaching to diatom cells may increase aggregate formation. Interestingly, photosynthetically inactivated T. weissflogii cells did not aggregate regardless of the presence of bacteria. Comparison of aggregate formation, TEP production, aggregate sinking velocity and solid hydrated density revealed remarkable differences. Both, photosynthetically active T. weissflogii and specific diatom-attaching bacteria were required for aggregation. It was concluded that interactions between heterotrophic bacteria and diatoms increased aggregate formation and particle sinking and thus may enhance the efficiency of the biological pump. PMID:20827289

Microbial aggregates in anaerobic wastewater treatment.

PubMed

Kosaric, N; Blaszczyk, R

1990-01-01

The phenomenon aggregation of anaerobic bacteria gives an opportunity to speed up the digestion rate during methanogenesis. The aggregates are mainly composed of methanogenic bacteria which convert acetate and H2/CO2 into methane. Other bacteria are also included in the aggregates but their concentration is rather small. The aggregates may also be formed during acetogenesis or even hydrolysis but such aggregates are not stable and disrupt quickly when not fed. A two stage process seems to be suitable when high concentrated solid waste must be treated. Special conditions are necessary to promote aggregate formation from methanogenic bacteria but aggregates once formed are stable without feeding even for a few years. The structure, texture and activity of bacterial aggregates depend on several parameters: (1)--temperature and pH, (2)--wastewater composition and (3)--hydrodynamic conditions within the reactor. The common influence of all these parameters is still rather unknown but some recommendations may be given. Temperature and pH should be maintained in the range which is optimal for methanogenic bacteria e.g. a temperature between 32 and 50 degrees C and a value pH between 6.5 and 7.5. Wastewaters should contain soluble wastes and the specific loading rate should be around one kgCOD(kgVSS)-1 d-1. The concentration of the elements influences aggregate composition and probably structure and texture. At high calcium concentration a change in the colour of the granules has been observed. Research is necessary to investigate the influence of other elements and organic toxicants on maintenance of the aggregates. Hydrodynamic conditions seem to influence the stability of the granules over long time periods. At low liquid stream rates, aggregates may starve and lysis within the aggregates is possible which results in hollowing of aggregates and their floating. At high liquid stream rates the aggregates may be disrupted and washed out of the reactor as a flocculent

Gut bacteria mediate aggregation in the German cockroach

PubMed Central

Wada-Katsumata, Ayako; Zurek, Ludek; Nalyanya, Godfrey; Roelofs, Wendell L.; Zhang, Aijun; Schal, Coby

2015-01-01

Aggregation of the German cockroach, Blattella germanica, is regulated by fecal aggregation agents (pheromones), including volatile carboxylic acids (VCAs). We demonstrate that the gut microbial community contributes to production of these semiochemicals. Chemical analysis of the fecal extract of B. germanica revealed 40 VCAs. Feces from axenic cockroaches (no microorganisms in the alimentary tract) lacked 12 major fecal VCAs, and 24 of the remaining compounds were represented at extremely low amounts. Olfactory and aggregation bioassays demonstrated that nymphs strongly preferred the extract of control feces over the fecal extract of axenic cockroaches. Additionally, nymphs preferred a synthetic blend of 6 fecal VCAs over a solvent control or a previously identified VCA blend. To test whether gut bacteria contribute to the production of fecal aggregation agents, fecal aerobic bacteria were cultured, isolated, and identified. Inoculation of axenic cockroaches with individual bacterial taxa significantly rescued the aggregation response to the fecal extract, and inoculation with a mix of six bacterial isolates was more effective than with single isolates. The results indicate that the commensal gut microbiota contributes to production of VCAs that act as fecal aggregation agents and that cockroaches discriminate among the complex odors that emanate from a diverse microbial community. Our results highlight the pivotal role of gut bacteria in mediating insect–insect communication. Moreover, because the gut microbial community reflects the local environment, local plasticity in fecal aggregation pheromones enables colony-specific odors and fidelity to persistent aggregation sites. PMID:26644557

Bacterial oxidation of dibromomethane and methyl bromide in natural waters and enrichment cultures

USGS Publications Warehouse

Goodwin, K.D.; Schaefer, J.K.; Oremland, R.S.

1998-01-01

Bacterial oxidation of 14CH2Br2 and 14CH3Br was measured in freshwater, estuarine, seawater, and hypersaline-alkaline samples. In general, bacteria from the various sites oxidized similar amounts of 14CH2Br2 and comparatively less 14CH3Br. Bacterial oxidation of 14CH3Br was rapid in freshwater samples compared to bacterial oxidation of 14CH3Br in more saline waters. Freshwater was also the only site in which methyl fluoride-sensitive bacteria (e.g., methanotrophs or nitrifiers) governed brominated methane oxidation. Half-life calculations indicated that bacterial oxidation of CH2Br2 was potentially significant in all of the waters tested. In contrast, only in freshwater was bacterial oxidation of CH3Br as fast as chemical removal. The values calculated for more saline sites suggested that bacterial oxidation of CH3Br was relatively slow compared to chemical and physical loss mechanisms. However, enrichment cultures demonstrated that bacteria in seawater can rapidly oxidize brominated methanes. Two distinct cultures of nonmethanotrophic methylotrophs were recovered; one of these cultures was able to utilize CH2Br2 as a sole carbon source, and the other was able to utilize CH3Br as a sole carbon source.

Analysis of microbial community and nitrogen transition with enriched nitrifying soil microbes for organic hydroponics.

PubMed

Saijai, Sakuntala; Ando, Akinori; Inukai, Ryuya; Shinohara, Makoto; Ogawa, Jun

2016-06-27

Nitrifying microbial consortia were enriched from bark compost in a water system by regulating the amounts of organic nitrogen compounds and by controlling the aeration conditions with addition of CaCO 3 for maintaining suitable pH. Repeated enrichment showed reproducible mineralization of organic nitrogen via the conversion of ammonium ions ([Formula: see text]) and nitrite ions ([Formula: see text]) into nitrate ions ([Formula: see text]). The change in microbial composition during the enrichment was investigated by PCR-DGGE analysis with a focus on prokaryote, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and eukaryote cell types. The microbial transition had a simple profile and showed clear relation to nitrogen ions transition. Nitrosomonas and Nitrobacter were mainly detected during [Formula: see text] and [Formula: see text] oxidation, respectively. These results revealing representative microorganisms acting in each ammonification and nitrification stages will be valuable for the development of artificial simple microbial consortia for organic hydroponics that consisted of identified heterotrophs and autotrophic nitrifying bacteria.

Effects of Cr(III) and CR(VI) on nitrification inhibition as determined by SOUR, function-specific gene expression and 16S rRNA sequence analysis of wastewater nitrifying enrichments

EPA Science Inventory

The effect of Cr(III) and Cr(VI) on ammonia oxidation, the transcriptional responses of functional genes involved in nitrification and changes in 16S rRNA level sequences were examined in nitrifying enrichment cultures. The nitrifying bioreactor was operated as a continuous react...

Ammonia oxidation pathways and nitrifier denitrification are significant sources of N2O and NO under low oxygen availability

PubMed Central

Zhu, Xia; Burger, Martin; Doane, Timothy A.; Horwath, William R.

2013-01-01

The continuous increase of nitrous oxide (N2O) abundance in the atmosphere is a global concern. Multiple pathways of N2O production occur in soil, but their significance and dependence on oxygen (O2) availability and nitrogen (N) fertilizer source are poorly understood. We examined N2O and nitric oxide (NO) production under 21%, 3%, 1%, 0.5%, and 0% (vol/vol) O2 concentrations following urea or ammonium sulfate [(NH4)2SO4] additions in loam, clay loam, and sandy loam soils that also contained ample nitrate. The contribution of the ammonia (NH3) oxidation pathways (nitrifier nitrification, nitrifier denitrification, and nitrification-coupled denitrification) and heterotrophic denitrification (HD) to N2O production was determined in 36-h incubations in microcosms by 15N-18O isotope and NH3 oxidation inhibition (by 0.01% acetylene) methods. Nitrous oxide and NO production via NH3 oxidation pathways increased as O2 concentrations decreased from 21% to 0.5%. At low (0.5% and 3%) O2 concentrations, nitrifier denitrification contributed between 34% and 66%, and HD between 34% and 50% of total N2O production. Heterotrophic denitrification was responsible for all N2O production at 0% O2. Nitrifier denitrification was the main source of N2O production from ammonical fertilizer under low O2 concentrations with urea producing more N2O than (NH4)2SO4 additions. These findings challenge established thought attributing N2O emissions from soils with high water content to HD due to presumably low O2 availability. Our results imply that management practices that increase soil aeration, e.g., reducing compaction and enhancing soil structure, together with careful selection of fertilizer sources and/or nitrification inhibitors, could decrease N2O production in agricultural soils. PMID:23576736

Ammonia oxidation pathways and nitrifier denitrification are significant sources of N2O and NO under low oxygen availability.

PubMed

Zhu, Xia; Burger, Martin; Doane, Timothy A; Horwath, William R

2013-04-16

The continuous increase of nitrous oxide (N2O) abundance in the atmosphere is a global concern. Multiple pathways of N2O production occur in soil, but their significance and dependence on oxygen (O2) availability and nitrogen (N) fertilizer source are poorly understood. We examined N2O and nitric oxide (NO) production under 21%, 3%, 1%, 0.5%, and 0% (vol/vol) O2 concentrations following urea or ammonium sulfate [(NH4)2SO4] additions in loam, clay loam, and sandy loam soils that also contained ample nitrate. The contribution of the ammonia (NH3) oxidation pathways (nitrifier nitrification, nitrifier denitrification, and nitrification-coupled denitrification) and heterotrophic denitrification (HD) to N2O production was determined in 36-h incubations in microcosms by (15)N-(18)O isotope and NH3 oxidation inhibition (by 0.01% acetylene) methods. Nitrous oxide and NO production via NH3 oxidation pathways increased as O2 concentrations decreased from 21% to 0.5%. At low (0.5% and 3%) O2 concentrations, nitrifier denitrification contributed between 34% and 66%, and HD between 34% and 50% of total N2O production. Heterotrophic denitrification was responsible for all N2O production at 0% O2. Nitrifier denitrification was the main source of N2O production from ammonical fertilizer under low O2 concentrations with urea producing more N2O than (NH4)2SO4 additions. These findings challenge established thought attributing N2O emissions from soils with high water content to HD due to presumably low O2 availability. Our results imply that management practices that increase soil aeration, e.g., reducing compaction and enhancing soil structure, together with careful selection of fertilizer sources and/or nitrification inhibitors, could decrease N2O production in agricultural soils.

A sensitive crude oil bioassay indicates that oil spills potentially induce a change of major nitrifying prokaryotes from the archaea to the bacteria.

PubMed

Urakawa, Hidetoshi; Garcia, Juan C; Barreto, Patricia D; Molina, Gabriela A; Barreto, Jose C

2012-05-01

The sensitivity of nitrifiers to crude oil released by the BP Deepwater Horizon oil spill in Gulf of Mexico was examined using characterized ammonia-oxidizing bacteria and archaea to develop a bioassay and to gain further insight into the ecological response of these two groups of microorganisms to marine oil spills. Inhibition of nitrite production was observed among all the tested ammonia-oxidizing organisms at 100 ppb crude oil. Nitrosopumilus maritimus, a cultured representative of the abundant Marine Group I Archaea, showed 20% inhibition at 1 ppb, a much greater degree of sensitivity to petroleum than the tested ammonia-oxidizing and heterotrophic bacteria. The differing susceptibility may have ecological significance since a shift to bacterial dominance in response to an oil spill could potentially persist and alter trophic interactions influenced by availability of different nitrogen species. Copyright © 2012 Elsevier Ltd. All rights reserved.

Using bacterial inclusion bodies to screen for amyloid aggregation inhibitors.

PubMed

Villar-Piqué, Anna; Espargaró, Alba; Sabaté, Raimon; de Groot, Natalia S; Ventura, Salvador

2012-05-03

The amyloid-β peptide (Aβ42) is the main component of the inter-neuronal amyloid plaques characteristic of Alzheimer's disease (AD). The mechanism by which Aβ42 and other amyloid peptides assemble into insoluble neurotoxic deposits is still not completely understood and multiple factors have been reported to trigger their formation. In particular, the presence of endogenous metal ions has been linked to the pathogenesis of AD and other neurodegenerative disorders. Here we describe a rapid and high-throughput screening method to identify molecules able to modulate amyloid aggregation. The approach exploits the inclusion bodies (IBs) formed by Aβ42 when expressed in bacteria. We have shown previously that these aggregates retain amyloid structural and functional properties. In the present work, we demonstrate that their in vitro refolding is selectively sensitive to the presence of aggregation-promoting metal ions, allowing the detection of inhibitors of metal-promoted amyloid aggregation with potential therapeutic interest. Because IBs can be produced at high levels and easily purified, the method overcomes one of the main limitations in screens to detect amyloid modulators: the use of expensive and usually highly insoluble synthetic peptides.

Synthesis, aggregation and spectroscopic studies of novel water soluble metal free, zinc, copper and magnesium phthalocyanines and investigation of their anti-bacterial properties

NASA Astrophysics Data System (ADS)

Bayrak, Rıza; Akçay, Hakkı Türker; Beriş, Fatih Şaban; Şahin, Ertan; Bayrak, Hacer; Demirbaş, Ümit

2014-12-01

In this study, novel phthalonitrile derivative (3) was synthesized by the reaction between 4-nitrophthalonitrile (2) and a triazole derivative (1) containing pyridine moiety. Crystal structure of compound (3) was characterized by X-ray diffraction. New metal free and metallo-phthalocyanine complexes (Zn, Cu, and Mg) were synthesized using the phthalonitrile derivative (3). Cationic derivatives of these phthalocyanines (5, 7, 9, and 11) were prepared from the non-ionic phthalocyanines (4, 6, 8, and 10). All proposed structures were supported by instrumental methods. The aggregation behaviors of the phthalocyanines (4-11) were investigated in different solvents such as dimethylsulfoxide (DMSO), N,N-dimethylformamide (DMF), chloroform and water. Water soluble cationic Pcs (5, 7, 9, and 11) aggregated in water and sodium dodecyl sulfate was used to prevent the aggregation. The second derivatives of the UV-Vis spectra of aggregated Pcs were used for analyzing the Q and B bands of aggregated species. Thermal behaviors of the phthalocyanines were also studied. In addition, anti-bacterial properties of the phthalocyanines were investigated. We used four gram negative and two gram positive bacteria to determine antibacterial activity of these compounds. Compound 7 has the best activity against the all bacteria with 125 μg/mL of MIC value. Compounds 4, 6, and 10 have the similar effect on the bacteria with 250 μg/mL of MIC value.

Removal of pharmaceutical and personal care products (PPCPs) under nitrifying and denitrifying conditions.

PubMed

Suarez, Sonia; Lema, Juan M; Omil, Francisco

2010-05-01

The contribution of volatilization, sorption and transformation to the removal of 16 Pharmaceutical and Personal Care Products (PPCPs) in two lab-scale conventional activated sludge reactors, working under nitrifying (aerobic) and denitrifying (anoxic) conditions for more than 1.5 years, have been assessed. Pseudo-first order biological degradation rate constants (k(biol)) were calculated for the selected compounds in both reactors. Faster degradation kinetics were measured in the nitrifying reactor compared to the denitrifying system for the majority of PPCPs. Compounds could be classified according to their k(biol) into very highly (k(biol)>5Lg(SS)(-1)d(-1)), highly (175%) and anoxic (>65%) conditions, whereas naproxen (NPX), ethinylestradiol (EE2), roxithromycin (ROX) and erythromycin (ERY) were only significantly transformed in the aerobic reactor (>80%). The anti-depressant citalopram (CTL) was moderately biotransformed under both, aerobic and anoxic conditions (>60% and >40%, respectively). Some compounds, as carbamazepine (CBZ), diazepam (DZP), sulfamethoxazole (SMX) and trimethoprim (TMP), manifested high resistance to biological transformation. Solids Retention Time (SRT(aerobic) >50d and <50d; SRT(anoxic) >20d and <20d) had a slightly positive effect on the removal of FLX, NPX, CTL, EE2 and natural estrogens (increase in removal efficiencies <10%). Removal of diclofenac (DCF) in the aerobic reactor was positively affected by the development of nitrifying biomass and increased from 0% up to 74%. Similarly, efficient anoxic transformation of ibuprofen (75%) was observed after an adaptation period of 340d. Temperature (16-26 degrees C) only had a slight effect on the removal of

Interaction of multiple biomimetic antimicrobial polymers with model bacterial membranes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baul, Upayan, E-mail: upayanb@imsc.res.in; Vemparala, Satyavani, E-mail: vani@imsc.res.in; Kuroda, Kenichi, E-mail: kkuroda@umich.edu

Using atomistic molecular dynamics simulations, interaction of multiple synthetic random copolymers based on methacrylates on prototypical bacterial membranes is investigated. The simulations show that the cationic polymers form a micellar aggregate in water phase and the aggregate, when interacting with the bacterial membrane, induces clustering of oppositely charged anionic lipid molecules to form clusters and enhances ordering of lipid chains. The model bacterial membrane, consequently, develops lateral inhomogeneity in membrane thickness profile compared to polymer-free system. The individual polymers in the aggregate are released into the bacterial membrane in a phased manner and the simulations suggest that the most probablemore » location of the partitioned polymers is near the 1-palmitoyl-2-oleoyl-phosphatidylglycerol (POPG) clusters. The partitioned polymers preferentially adopt facially amphiphilic conformations at lipid-water interface, despite lacking intrinsic secondary structures such as α-helix or β-sheet found in naturally occurring antimicrobial peptides.« less

Aeromonas species exhibit aggregative adherence to HEp-2 cells.

PubMed Central

Neves, M S; Nunes, M P; Milhomem, A M

1994-01-01

Clinical and environmental isolates of Aeromonas species (five A. hydrophila isolates, three A. caviae isolates, and two A. sobria isolates) were tested for their adherence to HEp-2 cells. Clinical isolates of A. hydrophila and A. sobria exhibited aggregative adherence similar to that presented by enteroadherent-aggregative Escherichia coli. Bacterial aggregates adhered to cells with a typical "stacked-brick" appearance. In contrast, A. caviae strains showed a diffuse adherence pattern. Images PMID:8027331

The cell aggregating propensity of probiotic actinobacterial isolates: isolation and characterization of the aggregation inducing peptide pheromone.

PubMed

Muthu Selvam, Ramu; Vinothini, Gopal; Palliyarai Thaiyammal, Sethuramalingam; Latha, Selvanathan; Chinnathambi, Arunachalam; Dhanasekaran, Dharumadurai; Padmanabhan, Parasuraman; Ali Alharbi, Sulaiman; Archunan, Govindaraju

2016-01-01

The auto-aggregating ability of a probiotic is a prerequisite for colonization and protection of the gastrointestinal tract, whereas co-aggregation provides a close interaction with pathogenic bacteria. Peptide pheromone mediated signaling has been studied in several systems. However, it has not yet been explored in prokaryotes, especially actinobacteria. Hence, in the present study, the diffusible aggregation promoting factor was purified from the culture supernatant of a potent actinobacterial probiont and characterized using 20 different actinobacterial cultures isolated from the gut region of chicken and goat. The results showed that the pheromone-like compound induces the aggregation propensity of treated isolates. The factor was found to be a heat stable, acidic pH resistant, low molecular weight peptide which enhances the biofilm forming ability of other actinobacterial isolates. The aggregation promoting factor represents a bacterial sex factor (pheromone) and its characterization confirms its usage in the probiotic formulation.

Multiscale simulation of red blood cell aggregation

NASA Astrophysics Data System (ADS)

Bagchi, P.; Popel, A. S.

2004-11-01

In humans and other mammals, aggregation of red blood cells (RBC) is a major determinant to blood viscosity in microcirculation under physiological and pathological conditions. Elevated levels of aggregation are often related to cardiovascular diseases, bacterial infection, diabetes, and obesity. Aggregation is a multiscale phenomenon that is governed by the molecular bond formation between adjacent cells, morphological and rheological properties of the cells, and the motion of the extra-cellular fluid in which the cells circulate. We have developed a simulation technique using front tracking methods for multiple fluids that includes the multiscale characteristics of aggregation. We will report the first-ever direct computer simulation of aggregation of deformable cells in shear flows. We will present results on the effect of shear rate, strength of the cross-bridging bonds, and the cell rheological properties on the rolling motion, deformation and subsequent breakage of an aggregate.

Nitrifier-induced denitrification is an important source of soil nitrous oxide and can be inhibited by a nitrification inhibitor 3,4-dimethylpyrazole phosphate.

PubMed

Shi, Xiuzhen; Hu, Hang-Wei; Zhu-Barker, Xia; Hayden, Helen; Wang, Juntao; Suter, Helen; Chen, Deli; He, Ji-Zheng

2017-12-01

Soil ecosystem represents the largest contributor to global nitrous oxide (N 2 O) production, which is regulated by a wide variety of microbial communities in multiple biological pathways. A mechanistic understanding of these N 2 O production biological pathways in complex soil environment is essential for improving model performance and developing innovative mitigation strategies. Here, combined approaches of the 15 N- 18 O labelling technique, transcriptome analysis, and Illumina MiSeq sequencing were used to identify the relative contributions of four N 2 O pathways including nitrification, nitrifier-induced denitrification (nitrifier denitrification and nitrification-coupled denitrification) and heterotrophic denitrification in six soils (alkaline vs. acid soils). In alkaline soils, nitrification and nitrifier-induced denitrification were the dominant pathways of N 2 O production, and application of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) significantly reduced the N 2 O production from these pathways; this is probably due to the observed reduction in the expression of the amoA gene in ammonia-oxidizing bacteria (AOB) in the DMPP-amended treatments. In acid soils, however, heterotrophic denitrification was the main source for N 2 O production, and was not impacted by the application of DMPP. Our results provide robust evidence that the nitrification inhibitor DMPP can inhibit the N 2 O production from nitrifier-induced denitrification, a potential significant source of N 2 O production in agricultural soils. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Treatment of raw and ozonated oil sands process-affected water under decoupled denitrifying anoxic and nitrifying aerobic conditions: a comparative study.

PubMed

Xue, Jinkai; Zhang, Yanyan; Liu, Yang; Gamal El-Din, Mohamed

2016-11-01

Batch experiments were performed to evaluate biodegradation of raw and ozonated oil sands process-affected water (OSPW) under denitrifying anoxic and nitrifying aerobic conditions for 33 days. The results showed both the anoxic and aerobic conditions are effective in degrading OSPW classical and oxidized naphthenic acids (NAs) with the aerobic conditions demonstrating higher removal efficiency. The reactors under nitrifying aerobic condition reduced the total classical NAs of raw OSPW by 69.1 %, with better efficiency for species of higher hydrophobicity. Compared with conventional aerobic reactor, nitrifying aerobic condition substantially shortened the NA degradation half-life to 16 days. The mild-dose ozonation remarkably accelerated the subsequent aerobic biodegradation of classical NAs within the first 14 days, especially for those with long carbon chains. Moreover, the ozone pretreatment enhanced the biological removal of OSPW classical NAs by leaving a considerably lower final residual concentration of 10.4 mg/L under anoxic conditions, and 5.7 mg/L under aerobic conditions. The combination of ozonation and nitrifying aerobic biodegradation removed total classical NAs by 76.5 % and total oxy-NAs (O3-O6) by 23.6 %. 454 Pyrosequencing revealed that microbial species capable of degrading recalcitrant hydrocarbons were dominant in all reactors. The most abundant genus in the raw and ozonated anoxic reactors was Thauera (~56 % in the raw OSPW anoxic reactor, and ~65 % in the ozonated OSPW anoxic reactor); whereas Rhodanobacter (~40 %) and Pseudomonas (~40 %) dominated the raw and ozonated aerobic reactors, respectively. Therefore, the combination of mild-dose ozone pretreatment and subsequent biological process could be a competent choice for OSPW treatment.

Mechanisms of N2O production in biological wastewater treatment under nitrifying and denitrifying conditions.

PubMed

Wunderlin, Pascal; Mohn, Joachim; Joss, Adriano; Emmenegger, Lukas; Siegrist, Hansruedi

2012-03-15

Nitrous oxide (N2O) is an important greenhouse gas and a major sink for stratospheric ozone. In biological wastewater treatment, microbial processes such as autotrophic nitrification and heterotrophic denitrification have been identified as major sources; however, the underlying pathways remain unclear. In this study, the mechanisms of N2O production were investigated in a laboratory batch-scale system with activated sludge for treating municipal wastewater. This relatively complex mixed population system is well representative for full-scale activated sludge treatment under nitrifying and denitrifying conditions. Under aerobic conditions, the addition of nitrite resulted in strongly nitrite-dependent N2O production, mainly by nitrifier denitrification of ammonia-oxidizing bacteria (AOB). Furthermore, N2O is produced via hydroxylamine oxidation, as has been shown by the addition of hydroxylamine. In both sets of experiments, N2O production was highest at the beginning of the experiment, then decreased continuously and ceased when the substrate (nitrite, hydroxylamine) had been completely consumed. In ammonia oxidation experiments, N2O peaked at the beginning of the experiment when the nitrite concentration was lowest. This indicates that N2O production via hydroxylamine oxidation is favored at high ammonia and low nitrite concentrations, and in combination with a high metabolic activity of ammonia-oxidizing bacteria (at 2 to 3 mgO2/l); the contribution of nitrifier denitrification by AOB increased at higher nitrite and lower ammonia concentrations towards the end of the experiment. Under anoxic conditions, nitrate reducing experiments confirmed that N2O emission is low under optimal growth conditions for heterotrophic denitrifiers (e.g. no oxygen input and no limitation of readily biodegradable organic carbon). However, N2O and nitric oxide (NO) production rates increased significantly in the presence of nitrite or low dissolved oxygen concentrations. Copyright �

The effects of nutrient chemotaxis on bacterial aggregation patterns with non-linear degenerate cross diffusion

NASA Astrophysics Data System (ADS)

Leyva, J. Francisco; Málaga, Carlos; Plaza, Ramón G.

2013-11-01

This paper studies a reaction-diffusion-chemotaxis model for bacterial aggregation patterns on the surface of thin agar plates. It is based on the non-linear degenerate cross diffusion model proposed by Kawasaki et al. (1997) [5] and it includes a suitable nutrient chemotactic term compatible with such type of diffusion, as suggested by Ben-Jacob et al. (2000) [20]. An asymptotic estimation predicts the growth velocity of the colony envelope as a function of both the nutrient concentration and the chemotactic sensitivity. It is shown that the growth velocity is an increasing function of the chemotactic sensitivity. High resolution numerical simulations using Graphic Processing Units (GPUs), which include noise in the diffusion coefficient for the bacteria, are presented. The numerical results verify that the chemotactic term enhances the velocity of propagation of the colony envelope. In addition, the chemotaxis seems to stabilize the formation of branches in the soft-agar, low-nutrient regime.

Synthesis, aggregation and spectroscopic studies of novel water soluble metal free, zinc, copper and magnesium phthalocyanines and investigation of their anti-bacterial properties.

PubMed

Bayrak, Rıza; Akçay, Hakkı Türker; Beriş, Fatih Şaban; Sahin, Ertan; Bayrak, Hacer; Demirbaş, Ümit

2014-12-10

In this study, novel phthalonitrile derivative (3) was synthesized by the reaction between 4-nitrophthalonitrile (2) and a triazole derivative (1) containing pyridine moiety. Crystal structure of compound (3) was characterized by X-ray diffraction. New metal free and metallo-phthalocyanine complexes (Zn, Cu, and Mg) were synthesized using the phthalonitrile derivative (3). Cationic derivatives of these phthalocyanines (5, 7, 9, and 11) were prepared from the non-ionic phthalocyanines (4, 6, 8, and 10). All proposed structures were supported by instrumental methods. The aggregation behaviors of the phthalocyanines (4-11) were investigated in different solvents such as dimethylsulfoxide (DMSO), N,N-dimethylformamide (DMF), chloroform and water. Water soluble cationic Pcs (5, 7, 9, and 11) aggregated in water and sodium dodecyl sulfate was used to prevent the aggregation. The second derivatives of the UV-Vis spectra of aggregated Pcs were used for analyzing the Q and B bands of aggregated species. Thermal behaviors of the phthalocyanines were also studied. In addition, anti-bacterial properties of the phthalocyanines were investigated. We used four gram negative and two gram positive bacteria to determine antibacterial activity of these compounds. Compound 7 has the best activity against the all bacteria with 125μg/mL of MIC value. Compounds 4, 6, and 10 have the similar effect on the bacteria with 250μg/mL of MIC value. Copyright © 2014 Elsevier B.V. All rights reserved.

Assessing carbon and nitrogen removal in a novel anoxic-aerobic cyanobacterial-bacterial photobioreactor configuration with enhanced biomass sedimentation.

PubMed

de Godos, I; Vargas, V A; Guzmán, H O; Soto, R; García, B; García, P A; Muñoz, R

2014-09-15

The carbon and nitrogen removal potential of an innovative anoxic-aerobic photobioreactor configuration operated with both internal and external recyclings was evaluated under different cyanobacterial-bacterial sludge residence times (9-31 days) during the treatment of wastewaters with low C/N ratios. Under optimal operating conditions, the two-stage photobioreactor was capable of providing organic carbon and nitrogen removals over 95% and 90%, respectively. The continuous biomass recycling from the settler resulted in the enrichment and predominance of rapidly-settling cyanobacterial-bacterial flocs and effluent suspended solid concentrations lower than 35 mg VSS L(-1). These flocs exhibited sedimentation rates of 0.28-0.42 m h(-1) but sludge volumetric indexes of 333-430 ml/g. The decoupling between the hydraulic retention time and sludge retention time mediated by the external recycling also avoided the washout of nitrifying bacteria and supported process operation at biomass concentrations of 1000-1500 mg VSS L(-1). The addition of additional NaHCO3 to the process overcame the CO2 limitation resulting from the intense competition for inorganic carbon between cyanobacteria and nitrifying bacteria in the photobioreactor, which supported the successful implementation of a nitrification-denitrification process. Unexpectedly, this nitrification-denitrification process occurred both simultaneously in the photobioreactor alone (as a result of the negligible dissolved oxygen concentrations) and sequentially in the two-stage anoxic-aerobic configuration with internal NO3(-)/NO2(-) recycling. Copyright © 2014 Elsevier Ltd. All rights reserved.

Effects of reclamation years on composition and diversity of soil bacterial communities in Northwest China.

PubMed

Cheng, Zhibo; Zhang, Fenghua; Gale, William Jeffrey; Wang, Weichao; Sang, Wen; Yang, Haichang

2018-01-01

The objective of this study was to evaluate bacterial community structure and diversity in soil aggregate fractions when salinized farmland was reclaimed after >27 years of abandonment and then farmed again for 1, 5, 10, and 15 years. Illumina MiSeq high-throughput sequencing was performed to characterize the soil bacterial communities in 5 aggregate size classes in each treatment. The results indicated that reclamation significantly increased macro-aggregation (>0.25 mm), as well as soil organic C, available N, and available P. The 10-year field had the largest proportion (93.9%) of soil in the macro-aggregate size classes (i.e., >0.25 mm) and the highest soil electrical conductivity. The 5 most dominant phyla in the soil samples were Proteobacteria, Actinobacteria, Gemmatimonadetes, Acidobacteria, and Bacteroidetes. The phylogenetic diversity, Chao1, and Shannon indices increased after the abandoned land was reclaimed for farming, reaching maximums in the 15-year field. Among aggregate size classes, the 1-0.25 mm aggregates generally had the highest phylogenetic diversity, Chao1, and Shannon indices. Soil organic C and soil electrical conductivity were the main environmental factors affecting the soil bacterial communities. The composition and structure of the bacterial communities also varied significantly depending on soil aggregate size and time since reclamation.

What causes the spatial heterogeneity of bacterial flora in the intestine of zebrafish larvae?

PubMed

Yang, Jinyou; Shimogonya, Yuji; Ishikawa, Takuji

2018-06-07

Microbial flora in the intestine has been thoroughly investigated, as it plays an important role in the health of the host. Jemielita et al. (2014) showed experimentally that Aeromonas bacteria in the intestine of zebrafish larvae have a heterogeneous spatial distribution. Although bacterial aggregation is important biologically and clinically, there is no mathematical model describing the phenomenon and its mechanism remains largely unknown. In this study, we developed a computational model to describe the heterogeneous distribution of bacteria in the intestine of zebrafish larvae. The results showed that biological taxis could cause the bacterial aggregation. Intestinal peristalsis had the effect of reducing bacterial aggregation through mixing function. Using a scaling argument, we showed that the taxis velocity of bacteria must be larger than the sum of the diffusive velocity and background bulk flow velocity to induce bacterial aggregation. Our model and findings will be useful to further the scientific understanding of intestinal microbial flora. Copyright © 2018 Elsevier Ltd. All rights reserved.

Nitrifier Gene Abundance and Diversity in Sediments Impacted by Acid Mine Drainage

PubMed Central

Ramanathan, Bhargavi; Boddicker, Andrew M.; Roane, Timberley M.; Mosier, Annika C.

2017-01-01

Extremely acidic and metal-rich acid mine drainage (AMD) waters can have severe toxicological effects on aquatic ecosystems. AMD has been shown to completely halt nitrification, which plays an important role in transferring nitrogen to higher organisms and in mitigating nitrogen pollution. We evaluated the gene abundance and diversity of nitrifying microbes in AMD-impacted sediments: ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB). Samples were collected from the Iron Springs Mining District (Ophir, CO, United States) during early and late summer in 2013 and 2014. Many of the sites were characterized by low pH (<5) and high metal concentrations. Sequence analyses revealed AOA genes related to Nitrososphaera, Nitrosotalea, and Nitrosoarchaeum; AOB genes related to Nitrosomonas and Nitrosospira; and NOB genes related to Nitrospira. The overall abundance of AOA, AOB and NOB was examined using quantitative PCR (qPCR) amplification of the amoA and nxrB functional genes and 16S rRNA genes. Gene copy numbers ranged from 3.2 × 104 – 4.9 × 107 archaeal amoA copies ∗ μg DNA-1, 1.5 × 103 – 5.3 × 105 AOB 16S rRNA copies ∗ μg DNA-1, and 1.3 × 106 – 7.7 × 107 Nitrospira nxrB copies ∗ μg DNA-1. Overall, Nitrospira nxrB genes were found to be more abundant than AOB 16S rRNA and archaeal amoA genes in most of the sample sites across 2013 and 2014. AOB 16S rRNA and Nitrospira nxrB genes were quantified in sediments with pH as low as 3.2, and AOA amoA genes were quantified in sediments as low as 3.5. Though pH varied across all sites (pH 3.2–8.3), pH was not strongly correlated to the overall community structure or relative abundance of individual OTUs for any gene (based on CCA and Spearman correlations). pH was positivity correlated to the total abundance (qPCR) of AOB 16S rRNA genes, but not for any other genes. Metals were not correlated to the overall nitrifier community composition or abundance, but

Neisseria gonorrhoeae Aggregation Reduces Its Ceftriaxone Susceptibility.

PubMed

Wang, Liang-Chun; Litwin, Madeline; Sahiholnasab, Zahraossadat; Song, Wenxia; Stein, Daniel C

2018-06-15

Antibiotic resistance in Neisseria gonorrhoeae (GC) has become an emerging threat worldwide and heightens the need for monitoring treatment failures. N. gonorrhoeae , a gram-negative bacterium responsible for gonorrhea, infects humans exclusively and can form aggregates during infection. While minimal inhibitory concentration (MIC) tests are often used for determining antibiotic resistance development and treatment, the knowledge of the true MIC in individual patients and how it relates to this laboratory measure is not known. We examined the effect of aggregation on GC antibiotic susceptibility and the relationship between bacterial aggregate size and their antibiotic susceptibility. Aggregated GC have a higher survival rate when treated with ceftriaxone than non-aggregated GC, with bacteria in the core of the aggregates surviving the treatment. GC lacking opacity-associated protein or pili, or expressing a truncated lipooligosaccharide, three surface molecules that mediate GC-GC interactions, reduce both aggregation and ceftriaxone survival. This study demonstrates that the aggregation of N. gonorrhoeae can reduce the susceptibility to antibiotics, and suggests that antibiotic utilization can select for GC surface molecules that promote aggregation which in turn drive pathogen evolution. Inhibiting aggregation may be a potential way of increasing the efficacy of ceftriaxone treatment, consequently reducing treatment failure.

Monochloramine Cometabolism by Mixed-Culture Nitrifiers ...

EPA Pesticide Factsheets

The current research investigated monochloramine cometabolism by nitrifying mixed cultures grown under drinking water relevant conditions and harvested from sand-packed reactors before conducting suspended growth batch kinetic experiments. Three batch reactors were used in each experiment: (1) a positive control to estimate ammonia kinetic parameters, (2) a negative control to account for abiotic reactions, and (3) a cometabolism reactor to estimate cometabolism kinetic constants. Kinetic parameters were estimated in AQUASIM with a simultaneous fit to all experimental data. Cometabolism kinetics were best described by a first order model. Monochloramine cometabolism kinetics were similar to those of ammonia metabolism, and monochloramine cometabolism was a significant loss mechanism (30% of the observed monochloramine loss). These results demonstrated that monochloramine cometabolism occurred in mixed cultures similar to those found in drinking water distribution systems; thus, cometabolism may be a significant contribution to monochloramine loss during nitrification episodes in drinking water distribution systems. The results demonstrated that monochloramine cometabolism occurred in mixed cultures similar to those found in drinking water distribution systems; thus, cometabolism may be a significant contribution to monochloramine loss during nitrification episodes in drinking water distribution systems.

Characterization of the microbial community in a lotic environment to assess the effect of pollution on nitrifying and potentially pathogenic bacteria.

PubMed

Medeiros, J D; Araújo, L X; da Silva, V L; Diniz, C G; Cesar, D E; Del'Duca, A; Coelho, C M

2014-08-01

This study aimed to investigate microbes involved in the nitrogen cycle and potentially pathogenic bacteria from urban and rural sites of the São Pedro stream. Water samples were collected from two sites. A seasonal survey of bacterial abundance was conducted. The dissolved nutrient content was analysed. PCR and FISH analysis were performed to identify and quantify microbes involved in the nitrogen cycle and potentially pathogenic bacteria. The seasonal survey revealed that the bacterial abundance was similar along the year on the rural area but varied on the urban site. Higher concentration of dissolved nutrients in the urban area indicated a eutrophic system. Considering the nitrifying microbes, the genus Nitrobacter was found, especially in the urban area, and may act as the principal bacteria in converting nitrite into nitrate at this site. The molecular markers napA, amoA, and nfrA were more accumulated at the urban site, justifying the higher content of nutrients metabolised by these enzymes. Finally, high intensity of amplicons from Enterococcus, Streptococcus, Bacteroides/Prevotella/Porphyromonas, Salmonella, S. aureus, P. aeruginosa and the diarrheagenic lineages of E. coli were observed at the urban site. These results indicate a change in the structure of the microbial community imposed by anthrophic actions. The incidence of pathogenic bacteria in aquatic environments is of particular importance to public health, emphasising the need for sewage treatment to minimise the environmental impacts associated with urbanisation.

Production of NO2/-/ and N2O by nitrifying bacteria at reduced concentrations of oxygen

NASA Technical Reports Server (NTRS)

Goreau, T. J.; Kaplan, W. A.; Wofsy, S. C.; Mcelroy, M. B.; Valois, F. W.; Watson, S. W.

1980-01-01

The influence of oxygen concentration on the production of NO2(-) and N2O by nitrifying marine bacteria of the genus Nitrosomonas is investigated. Pure cultures of the ammonium-oxiding bacteria isolated from the Western Tropical Atlantic Ocean were grown at oxygen partial pressures from 0.005 to 0.2 atm, and concentrations of N2O in the air above the growth medium and dissolved NO2(-) were determined. Decreasing oxygen concentrations are observed to induce a marked decrease in NO2(-) production rates and increase in N2O evolution, leading to an increase of the relative yield of N2O with respect to NO2(-) from 0.3% to nearly 10%. Similar yields of N2O at atmospheric oxygen levels are found for nitrifying bacteria of the genera Nitrosomonas, Nitrosolobus, Nitrosospira and Nitrosococcus, while nitrite-oxydizing bacteria and a dinoflagellate did not produce detectable quantities of N2O. Results support the view that nitrification is a major source of N2O in the environment.

In situ nitrification rates and activity of present nitrifiers in the bottom water layer of two Baltic coastal zones affected by different riverine nutrient loads

NASA Astrophysics Data System (ADS)

Bartl, I.; Münster Happel, E.; Riemann, L.; Voss, M.

2016-02-01

Baltic coastal zones are among the most eutrophied in the world receiving high loads of nitrogen from riverine inputs. However, not only the loads but also the internal dynamics in coastal zones might have positive feedback on eutrophication through efficient remineralisation of organic material in the bottom water. Therefore, we studied nitrification, which is a vital remineralisation process, near the seafloor along with the community of nitrifying microorganisms. We hypothesize that a high nutrient and organic matter load leads to elevated ammonium concentrations in coastal waters and thus stimulates nitrification rates and alters the nitrifying community. Here we present results from 3 cruises combining nitrification rate measurements by 15N-incubations with sequence-based analyses of present and active nitrifiers in the bottom water of two sites in the Baltic Sea receiving different nutrient loads. The first results from the Bonus projects COCOA and BLUEPRINT indicate an increase of nitrification rates with depth as well as distance from the river mouth. In situ rates in the bottom water of the nutrient rich Vistula plume range from 53 to 197 nmol L-1 d-1 and from 10 to 646 nmol L-1 d-1 during winter and summer, respectively. In the nutrient poor Öre estuary rates increased significantly by 11 nmol L-1 d-1 from the river mouth to the outermost station. The relationship between nitrification rates, nitrifiers and trophic state of the coastal zone shall be discussed.

Towards revealing the structure of bacterial inclusion bodies.

PubMed

Wang, Lei

2009-01-01

Protein aggregation is a widely observed phenomenon in human diseases, biopharmaceutical production, and biological research. Protein aggregates are generally classified as highly ordered, such as amyloid fibrils, or amorphous, such as bacterial inclusion bodies. Amyloid fibrils are elongated filaments with diameters of 6-12 nm, they are comprised of residue-specific cross-beta structure, and display characteristic properties, such as binding with amyloid-specific dyes. Amyloid fibrils are associated with dozens of human pathological conditions, including Alzheimer disease and prion diseases. Distinguished from amyloid fibrils, bacterial inclusion bodies display apparent amorphous morphology. Inclusion bodies are formed during high-level recombinant protein production, and formation of inclusion bodies is a major concern in biotechnology. Despite of the distinctive morphological difference, bacterial inclusion bodies have been found to have some amyloid-like properties, suggesting that they might contain structures similar to amyloid-like fibrils. Recent structural data further support this hypothesis, and this review summarizes the latest progress towards revealing the structural details of bacterial inclusion bodies.

Estimation of nitrite in source-separated nitrified urine with UV spectrophotometry.

PubMed

Mašić, Alma; Santos, Ana T L; Etter, Bastian; Udert, Kai M; Villez, Kris

2015-11-15

Monitoring of nitrite is essential for an immediate response and prevention of irreversible failure of decentralized biological urine nitrification reactors. Although a few sensors are available for nitrite measurement, none of them are suitable for applications in which both nitrite and nitrate are present in very high concentrations. Such is the case in collected source-separated urine, stabilized by nitrification for long-term storage. Ultraviolet (UV) spectrophotometry in combination with chemometrics is a promising option for monitoring of nitrite. In this study, an immersible in situ UV sensor is investigated for the first time so to establish a relationship between UV absorbance spectra and nitrite concentrations in nitrified urine. The study focuses on the effects of suspended particles and saturation on the absorbance spectra and the chemometric model performance. Detailed analysis indicates that suspended particles in nitrified urine have a negligible effect on nitrite estimation, concluding that sample filtration is not necessary as pretreatment. In contrast, saturation due to very high concentrations affects the model performance severely, suggesting dilution as an essential sample preparation step. However, this can also be mitigated by simple removal of the saturated, lower end of the UV absorbance spectra, and extraction of information from the secondary, weaker nitrite absorbance peak. This approach allows for estimation of nitrite with a simple chemometric model and without sample dilution. These results are promising for a practical application of the UV sensor as an in situ nitrite measurement in a urine nitrification reactor given the exceptional quality of the nitrite estimates in comparison to previous studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Biological role of bacterial inclusion bodies: a model for amyloid aggregation.

PubMed

García-Fruitós, Elena; Sabate, Raimon; de Groot, Natalia S; Villaverde, Antonio; Ventura, Salvador

2011-07-01

Inclusion bodies are insoluble protein aggregates usually found in recombinant bacteria when they are forced to produce heterologous protein species. These particles are formed by polypeptides that cross-interact through sterospecific contacts and that are steadily deposited in either the cell's cytoplasm or the periplasm. An important fraction of eukaryotic proteins form inclusion bodies in bacteria, which has posed major problems in the development of the biotechnology industry. Over the last decade, the fine dissection of the quality control system in bacteria and the recognition of the amyloid-like architecture of inclusion bodies have provided dramatic insights on the dynamic biology of these aggregates. We discuss here the relevant aspects, in the interface between cell physiology and structural biology, which make inclusion bodies unique models for the study of protein aggregation, amyloid formation and prion biology in a physiologically relevant background. © 2011 The Authors Journal compilation © 2011 FEBS.

Effects of mechanical disintegration of activated sludge on the activity of nitrifying and denitrifying bacteria and phosphorus accumulating organisms.

PubMed

Zubrowska-Sudol, Monika; Walczak, Justyna

2014-09-15

The purpose of the study was to analyse the impact of hydrodynamic disintegration of thickened excess activated sludge, performed at different levels of energy density (70, 140 and 210 kJ/L), on the activity of microorganisms involved in nutrient removal from wastewater, i.e. nitrifiers, denitrifiers and phosphorus accumulating organisms (PAOs). Ammonium and nitrogen utilisation rates and phosphorus release rates for raw and disintegrated sludge were determined using batch tests. The experiment also included: 1) analysis of organic and nutrient compound release from activated sludge flocs, 2) determination of the sludge disintegration degree (DD), and 3) evaluation of respiratory activity of the biomass by using the oxygen uptake rate (OUR) batch test. It was shown that the activity degree of the examined groups of microorganisms depended on energy density and related sludge disintegration degree, and that inactivation of individual groups of microorganisms occurred at different values of DD. Least resistant to the destruction of activated sludge flocs turned out to be phosphorus accumulating organisms, while the most resistant were denitrifiers. A decrease of 20-40% in PAO activity was noted already at DD equal to 3-5%. The threshold values of DD, after crossing which the inactivation of nitrifiers and denitrifiers occurred, were equal to 8% and 10%, respectively. At lesser DD values an increase in the activity of these groups of microorganisms was observed, averaging 20.2-41.7% for nitrifiers and 9.98-36.3% for denitrifiers. Copyright © 2014 Elsevier Ltd. All rights reserved.

Indigenous Halomonas spp., the Potential Nitrifying Bacteria for Saline Ammonium Waste Water Treatment.

PubMed

Sangnoi, Yutthapong; Chankaew, Sunipa; O-Thong, Sompong

2017-01-01

Toxic nitrogen compounds are one cause decreasing of shrimp production and water pollution. Indigenous Halomonas spp., isolated from Pacific white shrimp farm are benefitted for saline ammonium waste water treatment. This study aimed to isolate the heterotrophic-halophilic Halomonas spp. and investigate their ammonium removal efficiency. Halomonas spp., were isolated by culturing of samples collected from shrimp farm into modified Pep-Beef-AOM medium. Ammonium converting ability was tested and monitored by nitrite reagent. Ammonium removal efficiency was measured by the standard colorimetric method. Identification and classification of Halomonas spp., were studied by morphological, physiological and biochemical characteristics as well as molecular information. There were 5 strains of heterotrophic-halophilic nitrifying bacteria including SKNB2, SKNB4, SKNB17, SKNB20 and SKNB22 were isolated. The identification result based on 16S rRNA sequence analysis indicated that all 5 strains were Halomonas spp., with sequence similarity values of 91-99 %. Ammonium removal efficiency of all strains showed a range of 23-71%. The production of nitrite was low detected of 0.01-0.15 mg-N L-1, while the amount of nitrate was almost undetectable. This might suggest that the indigenous Halomonas spp., as nitrifying bacteria involved biological nitrification process for decreasing and transforming of ammonia. Due to being heterotrophic, halophilic and ammonium removing bacteria, these Halomonas spp., could be developed for use in treatment of saline ammonium waste water.

Tracking and quantification of nitrifying bacteria in biofilm and mixed liquor of a partial nitrification MBBR pilot plant using fluorescence in situ hybridization.

PubMed

Abzazou, Tarik; Araujo, Rosa M; Auset, María; Salvadó, Humbert

2016-01-15

A moving bead biofilm reactor (MBBR) pilot plant was implemented as a partial nitrification process for pre-treatment of ammonium-rich liquors (676 ± 195 mg L(-1)), and studied for 479 days under variations in hydraulic retention time. The main purpose of this work, was the study of dynamics abundance of total bacteria and single-cells nitrifying bacteria belonging to ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in biofilms and mixed liquor of the plant. The microbial monitoring was successfully achieved using fluorescence in situ hybridization combined with flocs disaggregation protocol as a useful microbial monitoring tool. A partial nitrification process with a N-NH4(+) removal rate of about 38.6 ± 14.8% was successfully achieved at 211 days after start-up, with a clear dominance of AOB, which accounted for 11.3 ± 17.0% of total bacterial cells compared with only 2.1 ± 4.0% of NOB. The effluent obtained was subsequently supplied to an Anammox reactor for complete ammonium treatment. Copyright © 2015 Elsevier B.V. All rights reserved.

Development of alginate-based aggregate inoculants of Methylobacterium sp. and Azospirillum brasilense tested under in vitro conditions to promote plant growth.

PubMed

Joe, M M; Saravanan, V S; Islam, M R; Sa, T

2014-02-01

To develop co-aggregated bacterial inoculant comprising of Methylobacterium oryzae CBMB20/Methylobacterium suomiense CBMB120 strains with Azospirillum brasilense (CW903) strain and testing their efficiency as inoculants for plant growth promotion (PGP). Biofilm formation and co-aggregation efficiency was studied between A. brasilense CW903 and methylobacterial strains M. oryzae CBMB20 and M. suomiense CBMB120. Survival and release of these co-aggregated bacterial strains entrapped in alginate beads were assessed. PGP attributes of the co-aggregated bacterial inoculant were tested in tomato plants under water-stressed conditions. Results suggest that the biofilm formation efficiency of the CBMB20 and CBMB120 strains increased by 15 and 34%, respectively, when co-cultivated with CW903. Co-aggregation with CW903 enhanced the survivability of CBMB20 strain in alginate beads. Water stress index score showed least stress index in plants inoculated with CW903 and CBMB20 strains maintained as a co-aggregated inoculant. This study reports the development of co-aggregated cell inoculants containing M. oryzae CBMB20 and A. brasilense CW903 strains conferred better shelf life and stress abatement in inoculated tomato plants. These findings could be extended to other PGP bacterial species to develop multigeneric bioinoculants with multiple benefits for various crops. © 2013 The Society for Applied Microbiology.

Process optimization by decoupled control of key microbial populations: distribution of activity and abundance of polyphosphate-accumulating organisms and nitrifying populations in a full-scale IFAS-EBPR plant.

PubMed

Onnis-Hayden, Annalisa; Majed, Nehreen; Schramm, Andreas; Gu, April Z

2011-07-01

This study investigated the abundance and distribution of key functional microbial populations and their activities in a full-scale integrated fixed film activated sludge-enhanced biological phosphorus removal (IFAS-EBPR) process. Polyphosphate accumulating organisms (PAOs) including Accumulibacter and EBPR activities were predominately associated with the mixed liquor (>90%) whereas nitrifying populations and nitrification activity resided mostly (>70%) on the carrier media. Ammonia oxidizer bacteria (AOB) were members of the Nitrosomonas europaea/eutropha/halophila and the Nitrosomonas oligotropha lineages, while nitrite oxidizer bacteria (NOB) belonged to the Nitrospira genus. Addition of the carrier media in the hybrid activated sludge system increased the nitrification capacity and stability; this effect was much greater in the first IFAS stage than in the second one where the residual ammonia concentration becomes limiting. Our results show that IFAS-EBPR systems enable decoupling of solid residence time (SRT) control for nitrifiers and PAOs that require or prefer conflicting SRT values (e.g. >15 days required for nitrifiers and <5 days preferred for PAOs). Allowing the slow-growing nitrifiers to attach to the carrier media and the faster-growing phosphorus (P)-removing organisms (and other heterotrophs, e.g. denitrifiers) to be in the suspended mixed liquor (ML), the EBPR-IFAS system facilitates separate SRT controls and overall optimization for both N and P removal processes. Copyright © 2011 Elsevier Ltd. All rights reserved.

Superiority of a functional leukocyte adhesiveness/aggregation test over the white blood cell count to discriminate between mild and significant inflammatory response in patients with acute bacterial infections.

PubMed

Rogowski, Ori; Rotstein, Rivka; Zeltzer, David; Misgav, Sarit; Justo, Daniel; Avitzour, Daniel; Mardi, Tamar; Serov, Jacob; Arber, Nadir; Berliner, Shlomo; Shapira, Itzhak

2002-01-01

Electronic cell counters may underestimate the white blood cell count (WBCC) in the presence of aggregated leukocytes. In the present study we focused on the possibility of using a functional, as opposed to an anatomic, count to circumvent this eventual underestimation. A model of bacterial infection was used because of the importance of leukocytosis in the physician's clinical decision-making process. There were 35 patients with low C-reactive protein (CRP) concentrations (0.5-4.9 mg/dL), 45 with intermediate (5-9.9 mg/dL), and 120 with relatively high (>10 mg/dL) CRP concentrations. A significant (P=0.008) difference was noted between the state of leukocyte adhesiveness/aggregation in the peripheral blood of individuals with low CRP concentrations (3.5%+/-4.3%) and those with high CRP concentrations (7.4%+/-8%), while there was no significant difference in the respective number of WBCs per cubic millimeter (cmm) (11,600 +/- 5,500 and 14,000 +/- 7,200, respectively). We raise the possibility that a functional test might be superior over an anatomic count in patients with acute bacterial infection and a significant acute phase response. Copyright 2002 Wiley-Liss, Inc.

Genome Sequence of a Heterotrophic Nitrifier and Aerobic Denitrifier, Paracoccus denitrificans Strain ISTOD1, Isolated from Wastewater.

PubMed

Medhi, Kristina; Mishra, Arti; Thakur, Indu Shekhar

2018-04-12

We report here the draft genome sequence of Paracoccus denitrificans strain ISTOD1 of 4.9 Mb, isolated from wastewater. It has been identified as a heterotrophic nitrifying and aerobic denitrifying bacterium. Genomic analysis revealed genes related to nitrogen and phosphorus removal, showing that the strain holds potential for bioremediation and biorefinery uses. Copyright © 2018 Medhi et al.

Genome Sequence of a Heterotrophic Nitrifier and Aerobic Denitrifier, Paracoccus denitrificans Strain ISTOD1, Isolated from Wastewater

PubMed Central

Medhi, Kristina; Mishra, Arti

2018-01-01

ABSTRACT We report here the draft genome sequence of Paracoccus denitrificans strain ISTOD1 of 4.9 Mb, isolated from wastewater. It has been identified as a heterotrophic nitrifying and aerobic denitrifying bacterium. Genomic analysis revealed genes related to nitrogen and phosphorus removal, showing that the strain holds potential for bioremediation and biorefinery uses. PMID:29650568

The Role of Thin Aggregative Fimbriae on Pathogenic Bacterial Transport Through Porous Media

NASA Astrophysics Data System (ADS)

Salvucci, A. E.; Fuka, D. R.; Marjerison, R. D.; Hay, A. G.; Zhang, W.; Caballero, L. A.; Zevi, Y.; Richards, B. K.; Steenhuis, T. S.

2008-05-01

Pathogenic bacteria, such as Escherichia coli and Salmonella sp., are responsible for many deaths worldwide every year. Their survival in the natural environment is enhanced by the production of biofilms, which provide a resistance to environmental stresses. However, it remains unclear how these biofilms affect the bacterias' ability to move through the soil matrix and potentially contaminate groundwater or water from drainage systems. In this presentation, we discuss the role of thin aggregative fimbriae (curli), a key biofilm component, on transport through porous media. An experiment was performed consisting of 96 sand columns created using a deep-well microtiter plate. We used well-characterized strains of E. coli, one with the ability to form curli and one without. Pulsing the E. coli strains through the sand column, mimicking natural leaching processes, showed less transport, by greater retention, in the strains that produce curli versus those strains that do not. In addition, when cultured in conditions unfavorable to curli production, transport between strains did not differ significantly. These preliminary results indicate that curli, and to a larger extent biofilms, could be an important component influencing the transport of bacterial strains through the soil matrix. This determination of pathogens' ability to move through the environment, as related to how well they form biofilms, will facilitate a better understanding of the fate of pathogenic bacteria in the environment.

Towards revealing the structure of bacterial inclusion bodies

PubMed Central

2009-01-01

Protein aggregation is a widely observed phenomenon in human diseases, biopharmaceutical production, and biological research. Protein aggregates are generally classified as highly ordered, such as amyloid fibrils, or amorphous, such as bacterial inclusion bodies. Amyloid fibrils are elongated filaments with diameters of 6–12 nm, they are comprised of residue-specific cross-β structure, and display characteristic properties, such as binding with amyloid-specific dyes. Amyloid fibrils are associated with dozens of human pathological conditions, including Alzheimer disease and prion diseases. Distinguished from amyloid fibrils, bacterial inclusion bodies display apparent amorphous morphology. Inclusion bodies are formed during high-level recombinant protein production, and formation of inclusion bodies is a major concern in biotechnology. Despite of the distinctive morphological difference, bacterial inclusion bodies have been found to have some amyloid-like properties, suggesting that they might contain structures similar to amyloid-like fibrils. Recent structural data further support this hypothesis, and this review summarizes the latest progress towards revealing the structural details of bacterial inclusion bodies. PMID:19806034

The response of nitrifying microbial assemblages to ammonium (NH4+) enrichment from salmon farm activities in a northern Chilean Fjord

NASA Astrophysics Data System (ADS)

Elizondo-Patrone, Claudia; Hernández, Klaudia; Yannicelli, Beatriz; Olsen, Lasse Mork; Molina, Verónica

2015-12-01

The consequences of aquaculture include alterations in nitrogen cycling in aquatic environments that may lead to ecosystem degradation. Herein salmon aquaculture release of ammonium (NH4+) to the water column and its effects on natural archaea and bacteria ammonia-oxidizers (AOA and AOB) and nitrite-oxidizing bacteria (NOB) community structure were studied in the Comau fjord using molecular approaches, such as: cloning (AOA and AOB richness), qPCR for C. Nitrosopumilus maritimus (AOA) and Nitrospina sp. (NOB) abundance (DNA) and RT-qPCR only for Nitrospina sp activity (RNA). Sampling was carried out in brackish (0.7-25 salinity, <5 m depth) and marine (>30 salinity, 25 m depth) waters during contrasting salmon production periods: rest (winter 2012), growth and harvest (summer and winter 2013). During the rest period, the highest NH4+ concentration was observed at Vodudahue River, whereas during productive periods NH4+ accumulated in the brackish layer inside salmon cages and in the vicinty (up to 700 m distance from the cages). The nitrifier community from the fjord reference station (Stn-C) was characterized by C. N. maritimus (AOA) and Nitrosomonas sp. (AOB) sequences affiliated with cosmopolitan ecotypes (e.g., marine, freshwater, hydrothermal), maxima abundances of C. N. maritimus (AOA) and Nitrospina sp. and extreme ranges of Nitrospina sp. activity occurred in the brackish layer. During productive periods, abundances of C. N. maritimus were co-varied with NH4+ concentrations inside salmon cages (summer) and the adjacent areas (winter). Productive periods were characterized by lower abundances but more homogeneity between brackish and marine areas than for the Stn-C nitrifiers. The physiological state of Nitrospina sp. estimated from cDNA:DNA ratios indicated higher growth during winter 2013 associated with NH4+ enrichment derived from production and river input. Our results suggest that in Comau Fjord, NH4+ enrichment events occur during salmon production and

Amyloid-linked cellular toxicity triggered by bacterial inclusion bodies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gonzalez-Montalban, Nuria; Departament de Genetica i de Microbiologia, Universitat Autonoma de Barcelona, Bellaterra, 08193 Barcelona; Ciber de Bioingenieria, Biomateriales y Nanomedicina

The aggregation of proteins in the form of amyloid fibrils and plaques is the characteristic feature of some pathological conditions ranging from neurodegenerative disorders to systemic amyloidoses. The mechanisms by which the aggregation processes result in cell damage are under intense investigation but recent data indicate that prefibrillar aggregates are the most proximate mediators of toxicity rather than mature fibrils. Since it has been shown that prefibrillar forms of the nondisease-related misfolded proteins are highly toxic to cultured mammalian cells we have studied the cytoxicity associated to bacterial inclusion bodies that have been recently described as protein deposits presenting amyloid-likemore » structures. We have proved that bacterial inclusion bodies composed by a misfolding-prone {beta}-galactosidase fusion protein are clearly toxic for mammalian cells but the {beta}-galactosidase wild type enzyme forming more structured thermal aggregates does not impair cell viability, despite it also binds and enter into the cells. These results are in the line that the most cytotoxic aggregates are early prefibrilar assemblies but discard the hypothesis that the membrane destabilization is Key event to subsequent disruption of cellular processes, such as ion balance, oxidative state and the eventually cell death.« less

Removal of pharmaceutically active compounds in nitrifying-denitrifying plants.

PubMed

Suárez, S; Ramil, M; Omil, F; Lema, J M

2005-01-01

The behaviour of nine pharmaceutically active compounds (PhACs) of different diagnostic groups is studied during a nitrifying-denitrifying process in an activated sludge system. The compounds selected cover a wide range of frequently used substances such as anti-epileptics (carbamazepine), tranquillisers (diazepam), anti-depressants (fluoxetine and citalopram), anti-inflammatories (ibuprofen, naproxen and diclofenac) and estrogens (estradiol and ethinylestradiol). The main objective of this research is to investigate the effect of acclimation of biomass on the removal rates of these compounds, either by maintaining a high sludge retention time or at long-term operation. The removal rates achieved for nitrogen and carbon in the experimental unit exceed 90% and were not affected by the addition of PhACs. Carbamazepine, diazepam and diclofenac were only removed to a small extent. On the other hand, higher removal rates have been observed for naproxen and ibuprofen (68% and 82%), respectively.

Who contributes more to N2O emission during sludge bio-drying with two different aeration strategies, nitrifiers or denitrifiers?

PubMed

Zhang, Junya; Wang, Yuanyue; Yu, Dawei; Tong, Juan; Chen, Meixue; Sui, Qianwen; ChuLu, BuHe; Wei, Yuansong

2017-04-01

Global warming effects have drawn more and more attention to studying all sources and sinks of nitrous oxide (N 2 O). Sludge bio-drying, as an effective sludge treatment technology, is being adopted worldwide. In this study, two aeration strategies (piles I and II) were compared to investigate the primary contributors to N 2 O emission during sludge bio-drying through studying the evolution of functional genes involved in nitrification (amoA, hao, and nxrA) and denitrification (narG, nirS, nirK, norB, and nosZ) by quantitative PCR (qPCR). Results showed that the profile of N 2 O emission can be divided into three stages, traditional denitrification contributed largely to N 2 O emission at stage I (days 1-5), but N 2 O emission mainly happened at stage II (days 5-14) due to nitrifier denitrification and NH 2 OH accumulation by ammonia-oxidizing bacteria (AOB), accounting for 51.4% and 58.2% of total N 2 O emission for piles I and II, respectively. At stage III (days 14-21), nitrifier denitrification was inhibited because sludge bio-drying proceeded mainly by the physical aeration, thus N 2 O emission decreased and changed little. The improved aeration strategy availed pile I to reduce N 2 O emission much especially at stages II and III, respectively. These results indicated that nitrifier denitrification by AOB and biological NH 2 OH oxidation due to AOB made more contribution to N 2 O emission, and aeration strategy was crucial to mitigate N 2 O emission during sludge bio-drying.

A local PDE model of aggregation formation in bacterial colonies

NASA Astrophysics Data System (ADS)

Chavy-Waddy, Paul-Christopher; Kolokolnikov, Theodore

2016-10-01

We study pattern formation in a model of cyanobacteria motion recently proposed by Galante, Wisen, Bhaya and Levy. By taking a continuum limit of their model, we derive a novel fourth-order nonlinear parabolic PDE equation that governs the behaviour of the model. This PDE is {{u}t}=-{{u}xx}-{{u}xxxx}+α {{≤ft(\\frac{{{u}x}{{u}xx}}{u}\\right)}x} . We then derive the instability thresholds for the onset of pattern formation. We also compute analytically the spatial profiles of the steady state aggregation density. These profiles are shown to be of the form \\text{sec}{{\\text{h}}p} where the exponent p is related to the parameters of the model. Full numerical simulations give a favorable comparison between the continuum and the underlying discrete system, and show that the aggregation profiles are stable above the critical threshold.

Nitrification performance and microbial ecology of nitrifying bacteria in a full-scale membrane bioreactor treating TFT-LCD wastewater.

PubMed

Whang, Liang-Ming; Wu, Yi-Ju; Lee, Ya-Chin; Chen, Hong-Wei; Fukushima, Toshikazu; Chang, Ming-Yu; Cheng, Sheng-Shung; Hsu, Shu-Fu; Chang, Cheng-Huey; Shen, Wason; Huang, Chung Kai; Fu, Ryan; Chang, Barkley

2012-10-01

This study investigated nitrification performance and nitrifying community in one full-scale membrane bioreactor (MBR) treating TFT-LCD wastewater. For the A/O MBR system treating monoethanolamine (MEA) and dimethyl sulfoxide (DMSO), no nitrification was observed, due presumably to high organic loading, high colloidal COD, low DO, and low hydraulic retention time (HRT) conditions. By including additional A/O or O/A tanks, the A/O/A/O MBR and the O/A/O MBR were able to perform successful nitrification. The real-time PCR results for quantification of nitrifying populations showed a high correlation to nitrification performance, and can be a good indicator of stable nitrification. Terminal restriction fragment length polymorphism (T-RFLP) results of functional gene, amoA, suggest that Nitrosomonas oligotropha-like AOB seemed to be important to a good nitrification in the MBR system. In the MBR system, Nitrobacter- and Nitrospira-like NOB were both abundant, but the low nitrite environment is likely to promote the growth of Nitrospira-like NOB. Copyright © 2012 Elsevier Ltd. All rights reserved.

Assessment of bacterial and structural dynamics in aerobic granular biofilms

PubMed Central

Weissbrodt, David G.; Neu, Thomas R.; Kuhlicke, Ute; Rappaz, Yoan; Holliger, Christof

2013-01-01

Aerobic granular sludge (AGS) is based on self-granulated flocs forming mobile biofilms with a gel-like consistence. Bacterial and structural dynamics from flocs to granules were followed in anaerobic-aerobic sequencing batch reactors (SBR) fed with synthetic wastewater, namely a bubble column (BC-SBR) operated under wash-out conditions for fast granulation, and two stirred-tank enrichments of Accumulibacter (PAO-SBR) and Competibacter (GAO-SBR) operated at steady-state. In the BC-SBR, granules formed within 2 weeks by swelling of Zoogloea colonies around flocs, developing subsequently smooth zoogloeal biofilms. However, Zoogloea predominance (37–79%) led to deteriorated nutrient removal during the first months of reactor operation. Upon maturation, improved nitrification (80–100%), nitrogen removal (43–83%), and high but unstable dephosphatation (75–100%) were obtained. Proliferation of dense clusters of nitrifiers, Accumulibacter, and Competibacter from granule cores outwards resulted in heterogeneous bioaggregates, inside which only low abundance Zoogloea (<5%) were detected in biofilm interstices. The presence of different extracellular glycoconjugates detected by fluorescence lectin-binding analysis showed the complex nature of the intracellular matrix of these granules. In the PAO-SBR, granulation occurred within two months with abundant and active Accumulibacter populations (56 ± 10%) that were selected under full anaerobic uptake of volatile fatty acids and that aggregated as dense clusters within heterogeneous granules. Flocs self-granulated in the GAO-SBR after 480 days during a period of over-aeration caused by biofilm growth on the oxygen sensor. Granules were dominated by heterogeneous clusters of Competibacter (37 ± 11%). Zoogloea were never abundant in biomass of both PAO- and GAO-SBRs. This study showed that Zoogloea, Accumulibacter, and Competibacter affiliates can form granules, and that the granulation mechanisms rely on the dominant

Bacterial communities in full-scale wastewater treatment systems.

PubMed

Cydzik-Kwiatkowska, Agnieszka; Zielińska, Magdalena

2016-04-01

Bacterial metabolism determines the effectiveness of biological treatment of wastewater. Therefore, it is important to define the relations between the species structure and the performance of full-scale installations. Although there is much laboratory data on microbial consortia, our understanding of dependencies between the microbial structure and operational parameters of full-scale wastewater treatment plants (WWTP) is limited. This mini-review presents the types of microbial consortia in WWTP. Information is given on extracellular polymeric substances production as factor that is key for formation of spatial structures of microorganisms. Additionally, we discuss data on microbial groups including nitrifiers, denitrifiers, Anammox bacteria, and phosphate- and glycogen-accumulating bacteria in full-scale aerobic systems that was obtained with the use of molecular techniques, including high-throughput sequencing, to shed light on dependencies between the microbial ecology of biomass and the overall efficiency and functional stability of wastewater treatment systems. Sludge bulking in WWTPs is addressed, as well as the microbial composition of consortia involved in antibiotic and micropollutant removal.

Real-time monitoring of quorum sensing in 3D-printed bacterial aggregates using scanning electrochemical microscopy.

PubMed

Connell, Jodi L; Kim, Jiyeon; Shear, Jason B; Bard, Allen J; Whiteley, Marvin

2014-12-23

Microbes frequently live in nature as small, densely packed aggregates containing ∼10(1)-10(5) cells. These aggregates not only display distinct phenotypes, including resistance to antibiotics, but also, serve as building blocks for larger biofilm communities. Aggregates within these larger communities display nonrandom spatial organization, and recent evidence indicates that this spatial organization is critical for fitness. Studying single aggregates as well as spatially organized aggregates remains challenging because of the technical difficulties associated with manipulating small populations. Micro-3D printing is a lithographic technique capable of creating aggregates in situ by printing protein-based walls around individual cells or small populations. This 3D-printing strategy can organize bacteria in complex arrangements to investigate how spatial and environmental parameters influence social behaviors. Here, we combined micro-3D printing and scanning electrochemical microscopy (SECM) to probe quorum sensing (QS)-mediated communication in the bacterium Pseudomonas aeruginosa. Our results reveal that QS-dependent behaviors are observed within aggregates as small as 500 cells; however, aggregates larger than 2,000 bacteria are required to stimulate QS in neighboring aggregates positioned 8 μm away. These studies provide a powerful system to analyze the impact of spatial organization and aggregate size on microbial behaviors.

Light-induced aggregation of microbial exopolymeric substances.

PubMed

Sun, Luni; Xu, Chen; Zhang, Saijin; Lin, Peng; Schwehr, Kathleen A; Quigg, Antonietta; Chiu, Meng-Hsuen; Chin, Wei-Chun; Santschi, Peter H

2017-08-01

Sunlight can inhibit or disrupt the aggregation process of marine colloids via cleavage of high molecular weight compounds into smaller, less stable fragments. In contrast, some biomolecules, such as proteins excreted from bacteria can form aggregates via cross-linking due to photo-oxidation. To examine whether light-induced aggregation can occur in the marine environment, we conducted irradiation experiments on a well-characterized protein-containing exopolymeric substance (EPS) from the marine bacterium Sagitulla stellata. Our results show that after 1 h sunlight irradiation, the turbidity level of soluble EPS was 60% higher than in the dark control. Flow cytometry also confirmed that more particles of larger sized were formed by sunlight. In addition, we determined a higher mass of aggregates collected on filter in the irradiated samples. This suggests light can induce aggregation of this bacterial EPS. Reactive oxygen species hydroxyl radical and peroxide played critical roles in the photo-oxidation process, and salts assisted the aggregation process. The observation that Sagitulla stellata EPS with relatively high protein content promoted aggregation, was in contrast to the case where no significant differences were found in the aggregation of a non-protein containing phytoplankton EPS between the dark and light conditions. This, together with the evidence that protein-to-carbohydrate ratio of aggregates formed under light condition is significantly higher than that formed under dark condition suggest that proteins are likely the important component for aggregate formation. Light-induced aggregation provides new insights into polymer assembly, marine snow formation, and the fate/transport of organic carbon and nitrogen in the ocean. Copyright © 2017 Elsevier Ltd. All rights reserved.

Studies on bacterial inclusion bodies.

PubMed

de Groot, Natalia S; Espargaró, Alba; Morell, Montserrat; Ventura, Salvador

2008-08-01

The field of protein misfolding and aggregation has become an extremely active area of research in recent years. Of particular interest is the deposition of polypeptides into inclusion bodies inside bacterial cells. One reason for this interest is that protein aggregation constitutes a major bottleneck in protein production and restricts the spectrum of protein-based drugs available for commercialization. Additionally, prokaryotic cells could provide a simple yet powerful system for studying the formation and prevention of toxic aggregates, such as those responsible for a number of degenerative diseases. Here, we review recent work that has challenged our understanding of the structure and physiology of inclusion bodies and provided us with a new view of intracellular protein deposition, which has important implications in microbiology, biomedicine and biotechnology.

The specific role of fungal community structure on soil aggregation and carbon sequestration: results from long-term field study in a paddy soil

NASA Astrophysics Data System (ADS)

Murugan, Rajasekaran; Kumar, Sanjay

2015-04-01

Soil aggregate stability is a crucial soil property that affects soil biota, biogeochemical processes and C sequestration. The relationship between soil aggregate stability and soil C cycling is well known but the influence of specific fungal community structure on this relationship is largely unknown in paddy soils. The aim of the present study was to evaluate the long-term fertilisation (mineral fertiliser-MIN; farmyard manure-FYM; groundnut oil cake-GOC) effects on soil fungal community shifts associated with soil aggregates under rice-monoculture (RRR) and rice-legume-rice (RLR) systems. Fungal and bacterial communities were characterized using phospholipid fatty acids, and glucosamine and muramic acid were used as biomarkers for fungal and bacterial residues, respectively. Microbial biomass C and N, fungal biomass and residues were significantly higher in the organic fertiliser treatments than in the MIN treatment, for all aggregate sizes under both crop rotation systems. In general, fungal/bacterial biomass ratio and fungal residue C/bacterial residue C ratio were significantly higher in macroaggregate fractions (> 2000 and 250-2000 μm) than in microaggregate fractions (53-250 and <53 μm). In both crop rotation systems, the long-term application of FYM and GOC led to increased accumulation of saprotrophic fungi (SF) in aggregate fractions > 2000 μm. In contrast, we found that arbuscular mycorrhizal fungi (AMF) was surprisingly higher in aggregate fractions > 2000 μm than in aggregate fraction 250-2000 μm under MIN treatment. The RLR system showed significantly higher AMF biomass and fungal residue C/ bacterial residue C ratio in both macroaggregate fractions compared to the RRR system. The strong relationships between SF, AMF and water stable aggregates shows the specific contribution of fungi community on soil aggregate stability. Our results highlight the fact that changes within fungal community structure play an important role in shaping the soil

Recovery of soil ammonia oxidation after long-term zinc exposure is not related to the richness of the bacterial nitrifying community.

PubMed

Ruyters, Stefan; Springael, Dirk; Smolders, Erik

2013-08-01

A soil sterilization-reinoculation approach was used to manipulate soil microbial diversity and to assess the effect of the diversity of the ammonia-oxidizing bacteria (AOB) on the recovery of the nitrifying community to metal stress (zinc). Gamma-irradiated soil was inoculated with 13 different combinations of up to 22 different soils collected worldwide to create varying degrees of AOB diversity. Two months after inoculation, AOB amoA DGGE based diversity (weighted richness) varied more than 10-fold among the 13 treatments, the largest value observed where the number of inocula had been largest. Subsequently, the 13 treatments were either or not amended with ZnCl2. Initially, Zn amendment completely inhibited nitrification. After 6 months of Zn exposure, recovery of the potential nitrification activity in the Zn amended soils ranged from <10 % to >100 % of the potential nitrification activity in the corresponding non-amended soils. This recovery was neither related to DGGE-based indices of AOB diversity nor to the AOB abundance assessed 2 months after inoculation (p > 0.05). However, recovery was significantly related (r = 0.75) to the potential nitrification rate before Zn amendment and only weakly to the number of soil inocula used in the treatments (r = 0.46). The lack of clear effects of AOB diversity on recovery may be related to an inherently sufficient diversity and functional redundancy of AOB communities in soil. Our data indicate that potential microbial activity can be a significant factor in recovery.

The structure of microbial community in aggregates of a typical chernozem aggregates under contrasting variants of its agricultural use

NASA Astrophysics Data System (ADS)

Ivanova, E. A.; Kutovaya, O. V.; Tkhakakhova, A. K.; Chernov, T. I.; Pershina, E. V.; Markina, L. G.; Andronov, E. E.; Kogut, B. M.

2015-11-01

The taxonomic structure of microbiomes in aggregates of different sizes from typical chernozems was investigated using sequencing of the 16S rRNA gene. The aggregate fractions of <0.25, 2-5, and >7 mm obtained by sieving of the soil samples at natural moisture were used for analysis. The highest prokaryote biomass (bacteria, archaea) was determined in the fractions <0.25 and aggregates 2-5 mm; the bacterial and archaeal biomass decreased in the following series: fallow > permanent black fallow > permanent winter wheat. The greatest number of fungi was recorded in the fraction <0.25 mm from the soils of the permanent black fallow and in all the studied aggregate fractions in the variant with permanent wheat. The system of agricultural use affected more significantly the structure of the prokaryote community in the chernozem than the size of aggregate fractions did. The most diverse microbial community was recorded in the soil samples of the fallow; the statistically significant maximums of the Shannon diversity indices and indices of phylogenetic diversity (PD) were recorded in the fractions <0.25 and 2-5 mm from the fallow soil. On the whole, the fine soil fractions (<0.25 mm) were characterized by higher diversity indices in comparison with those of the coarser aggregate fractions.

[Distribution Characteristics of Nitrifiers and Denitrifiers in the River Sediments of Tongling City].

PubMed

Cheng, Jian-hua; Dou, Zhi-yong; Sun, Qing-ye

2016-04-15

Rivers in mining areas were influenced by contaminants such as nitrogen, phosphorus and organic matter due to domestic and agricultural wastewater discharge in addition to pollutants caused by mining activities. In this study, surface sediment samples of rivers in Tongling city were collected to address the effect of season and pollution type on the abundance of nitrifiers and denitrifiers using quantitative polymerase chain reaction (QPCR) technique targeting at the ammonia monooxygenase (amoA) and nitrite reductase (nir) genes. The results showed that the average ahundance of ammonia oxidizing archaea (AGA) (ranging from 1.74 x 10⁵ to 1.45 x 10⁸ copies · g⁻¹) was 4.39 times that of ammonia oxidizing hacteria (AGH) (ranging from 1.39 x 10⁵ to 3.39 x 10⁷ copies · g⁻¹); and the average abundance of nirK gene (ranging from 4.45 x 10⁶ to 1.51 x 10⁸ copies · g) was almost a thirtieth part of nirS gene (ranging from 1.69 x 10⁷ to 8.55 x 10⁹ copies · g⁻¹). The abundance of AOA was higher in spring and autumn, and lower in summer and winter. And sediment AOB abundance was higher in spring and winter than in summer and autumn. Meanwhile, the abundance of nir genes was in the order of spring (nirS )/autumn (nirK) > summer > winter > autumn (nirS )/spring (nirK). Moreover, the abundance of bacterial and archaeal arnoA and nirS genes in sediments influenced by mine pollution was generally higher than that in sediments influenced by agricultural non-point pollution, whereas the abundance of nirK gene showed an opposite trend.

Profiling bacterial communities associated with sediment-based aquaculture bioremediation systems under contrasting redox regimes

NASA Astrophysics Data System (ADS)

Robinson, Georgina; Caldwell, Gary S.; Wade, Matthew J.; Free, Andrew; Jones, Clifford L. W.; Stead, Selina M.

2016-12-01

Deposit-feeding invertebrates are proposed bioremediators in microbial-driven sediment-based aquaculture effluent treatment systems. We elucidate the role of the sediment reduction-oxidation (redox) regime in structuring benthic bacterial communities, having direct implications for bioremediation potential and deposit-feeder nutrition. The sea cucumber Holothuria scabra was cultured on sediments under contrasting redox regimes; fully oxygenated (oxic) and redox stratified (oxic-anoxic). Taxonomically, metabolically and functionally distinct bacterial communities developed between the redox treatments with the oxic treatment supporting the greater diversity; redox regime and dissolved oxygen levels were the main environmental drivers. Oxic sediments were colonised by nitrifying bacteria with the potential to remediate nitrogenous wastes. Percolation of oxygenated water prevented the proliferation of anaerobic sulphate-reducing bacteria, which were prevalent in the oxic-anoxic sediments. At the predictive functional level, bacteria within the oxic treatment were enriched with genes associated with xenobiotics metabolism. Oxic sediments showed the greater bioremediation potential; however, the oxic-anoxic sediments supported a greater sea cucumber biomass. Overall, the results indicate that bacterial communities present in fully oxic sediments may enhance the metabolic capacity and bioremediation potential of deposit-feeder microbial systems. This study highlights the benefits of incorporating deposit-feeding invertebrates into effluent treatment systems, particularly when the sediment is oxygenated.

Profiling bacterial communities associated with sediment-based aquaculture bioremediation systems under contrasting redox regimes

PubMed Central

Robinson, Georgina; Caldwell, Gary S.; Wade, Matthew J.; Free, Andrew; Jones, Clifford L. W.; Stead, Selina M.

2016-01-01

Deposit-feeding invertebrates are proposed bioremediators in microbial-driven sediment-based aquaculture effluent treatment systems. We elucidate the role of the sediment reduction-oxidation (redox) regime in structuring benthic bacterial communities, having direct implications for bioremediation potential and deposit-feeder nutrition. The sea cucumber Holothuria scabra was cultured on sediments under contrasting redox regimes; fully oxygenated (oxic) and redox stratified (oxic-anoxic). Taxonomically, metabolically and functionally distinct bacterial communities developed between the redox treatments with the oxic treatment supporting the greater diversity; redox regime and dissolved oxygen levels were the main environmental drivers. Oxic sediments were colonised by nitrifying bacteria with the potential to remediate nitrogenous wastes. Percolation of oxygenated water prevented the proliferation of anaerobic sulphate-reducing bacteria, which were prevalent in the oxic-anoxic sediments. At the predictive functional level, bacteria within the oxic treatment were enriched with genes associated with xenobiotics metabolism. Oxic sediments showed the greater bioremediation potential; however, the oxic-anoxic sediments supported a greater sea cucumber biomass. Overall, the results indicate that bacterial communities present in fully oxic sediments may enhance the metabolic capacity and bioremediation potential of deposit-feeder microbial systems. This study highlights the benefits of incorporating deposit-feeding invertebrates into effluent treatment systems, particularly when the sediment is oxygenated. PMID:27941918

Meso and micro-scale response of post carbon removal nitrifying MBBR biofilm across carrier type and loading.

PubMed

Young, Bradley; Banihashemi, Bahman; Forrest, Daina; Kennedy, Kevin; Stintzi, Alain; Delatolla, Robert

2016-03-15

This study investigates the effects of three specific moving bed biofilm reactor (MBBR) carrier types and two surface area loading rates on biofilm thickness, morphology and bacterial community structure of post carbon removal nitrifying MBBR systems along with the effects of carrier type and loading on ammonia removal rates and effluent solids settleability. The meso and micro analyses show that the AOB kinetics vary based on loading condition, but irrespective of carrier type. The meso-scale response to increases in loading was shown to be an increase in biofilm thickness with higher surface area carriers being more inclined to develop and maintain thicker biofilms. The pore spaces of these higher surface area to volume carriers also demonstrated the potential to become clogged at higher loading conditions. Although the biofilm thickness increased during higher loading conditions, the relative percentages of both the embedded viable and non-viable cells at high and conventional loading conditions remained stable; indicating that the reduced ammonia removal kinetics observed during carrier clogging events is likely due to the observed reduction in the surface area of the attached biofilm. Microbial community analyses demonstrated that the dominant ammonia oxidizing bacteria for all carriers is Nitrosomonas while the dominant nitrite oxidizing bacteria is Nitrospira. The research showed that filamentous species were abundant under high loading conditions, which likely resulted in the observed reduction in effluent solids settleability at high loading conditions as opposed to conventional loading conditions. Although the settleability of the effluent solids was correlated to increases in abundances of filamentous organisms in the biofilm, analyzed using next generation sequencing, the ammonia removal rate was not shown to be directly correlated to specific meso or micro-scale characteristics. Instead post carbon removal MBBR ammonia removal kinetics were shown to be

Long-term tillage and nitrogen fertilization in maize influences the ammonia-oxidizing bacterial community

USDA-ARS?s Scientific Manuscript database

Nitrification is a biological oxidation of NH3 to NO2- and then to NO3-. Managing nitrifiers to increase nitrogen (N) fertilizer use efficiency, decrease NO3- leaching, and reduce NO and N2O emissions could benefit the environment. But one must first understand the structure of the nitrifier communi...

Application of a Novel Functional Gene Microarray to Probe the Functional Ecology of Ammonia Oxidation in Nitrifying Activated Sludge

PubMed Central

Short, Michael D.; Abell, Guy C. J.; Bodrossy, Levente; van den Akker, Ben

2013-01-01

We report on the first study trialling a newly-developed, functional gene microarray (FGA) for characterising bacterial and archaeal ammonia oxidisers in activated sludge. Mixed liquor (ML) and media biofilm samples from a full-scale integrated fixed-film activated sludge (IFAS) plant were analysed with the FGA to profile the diversity and relative abundance of ammonia-oxidising archaea and bacteria (AOA and AOB respectively). FGA analyses of AOA and AOB communities revealed ubiquitous distribution of AOA across all samples – an important finding for these newly-discovered and poorly characterised organisms. Results also revealed striking differences in the functional ecology of attached versus suspended communities within the IFAS reactor. Quantitative assessment of AOB and AOA functional gene abundance revealed a dominance of AOB in the ML and approximately equal distribution of AOA and AOB in the media-attached biofilm. Subsequent correlations of functional gene abundance data with key water quality parameters suggested an important functional role for media-attached AOB in particular for IFAS reactor nitrification performance and indicate possible functional redundancy in some IFAS ammonia oxidiser communities. Results from this investigation demonstrate the capacity of the FGA to resolve subtle ecological shifts in key microbial communities in nitrifying activated sludge and indicate its value as a tool for better understanding the linkages between the ecology and performance of these engineered systems. PMID:24155925

Chloraminated Drinking Water Distribution System Nitrification: Batch and Biofilm Inactivation Studies, Model Nitrifying Biofilm Investigations, and Evaluation of Operational Responses to Nitrification Episodes

EPA Science Inventory

Studies are currently underway to help fill knowledge gaps that exist in the general understanding of nitrification episodes. One of these gaps includes the need for growth and inactivation kinetic parameters for nitrifiers representative of those inhabiting distribution systems ...

[Bacterial diversity in sequencing batch biofilm reactor (SBBR) for landfill leachate treatment using PCR-DGGE].

PubMed

Xiao, Yong; Yang, Zhao-hui; Zeng, Guang-ming; Ma, Yan-he; Liu, You-sheng; Wang, Rong-juan; Xu, Zheng-yong

2007-05-01

For studying the bacterial diversity and the mechanism of denitrification in sequencing bath biofilm reactor (SBBR) treating landfill leachate to provide microbial evidence for technique improvements, total microbial DNA was extracted from samples which were collected from natural landfill leachate and biofilm of a SBBR that could efficiently remove NH4+ -N and COD of high concentration. 16S rDNA fragments were amplified from the total DNA successfully using a pair of universal bacterial 16S rDNA primer, GC341F and 907R, and then were used for denaturing gradient gel electrophoresis (DGGE) analysis. The bands in the gel were analyzed by statistical methods and excided from the gel for sequencing, and the sequences were used for homology analysis and then two phylogenetic trees were constructed using DNAStar software. Results indicated that the bacterial diversity of the biofilm in SBBR and the landfill leachate was abundant, and no obvious change of community structure happened during running in the biofilm, in which most bacteria came from the landfill leachate. There may be three different modes of denitrification in the reactor because several different nitrifying bacteria, denitrifying bacteria and anaerobic ammonia oxidation bacteria coexisted in it. The results provided some valuable references for studying microbiological mechanism of denitrification in SBBR.

Carrier effects on tertiary nitrifying moving bed biofilm reactor: An examination of performance, biofilm and biologically produced solids.

PubMed

Forrest, Daina; Delatolla, Robert; Kennedy, Kevin

2016-01-01

Increasingly stricter ammonia and nitrogen release regulations with respect to wastewater effluents are creating a need for tertiary treatment systems. The moving bed biofilm reactor (MBBR) is being considered as an upgrade option for an increasing number of wastewater treatment facilities due to its small footprint and ease of operation. Despite the MBBRs creation as a system to remove nitrogen, recent research on MBBR systems showing that the system's performance is directly related to carrier surface area and is irrespective of carrier shape and type has been performed exclusively on chemical oxygen demand (COD) removal systems. Furthermore, the influence of carrier type on the solids produced by MBBR systems has also been exclusively studied for COD removal systems. This work investigates the effects of three specific carrier types on ammonia removal rates, biofilm morphology, along with solids production and settleability of tertiary nitrifying MBBR systems. The study concludes that carrier type has no significant effect on tertiary nitrifying MBBR system performance under steady, moderate loading conditions. The research does however highlight the propensity of greater surface area to volume carriers to become clogged under high loading conditions and that the high surface area carriers investigated in this study required longer adjustment periods to changes in loading after becoming clogged.

Simazine biodegradation in soil: analysis of bacterial community structure by in situ hybridization.

PubMed

Caracciolo, Anna Barra; Grenni, Paola; Ciccoli, Roberto; Di Landa, Giuseppe; Cremisini, Carlo

2005-09-01

Pesticide and nitrate contamination of soil and groundwater from agriculture is an environmental and public health concern worldwide. Simazine, 6-chloro-N2,N4-diethyl-1,3,5-triazine-2,4-diamine, is a triazine herbicide used in agriculture for selective weed control with several types of crops and it is frequently applied to soils receiving N-fertilizers. Degradation experiments were performed in the laboratory to assess whether the biodegradation of simazine in soil may be influenced by the presence of urea. Simazine degradation rates under different experimental conditions (presence/absence of urea, microbiologically active/sterilized soil) were assessed together with the formation, degradation and transformation of its main metabolites in soil. Simazine degradation was affected by the presence of urea, in terms both of a smaller half-life (t(1/2)) and of a higher amount of desethyl-simazine formed. The soil bacterial community was also studied. Microbial abundances were determined by epifluorescence direct counting. Moreover in situ hybridization with rRNA-targeted fluorescent oligonucleotide probes was used to analyze the bacterial community structure. Fluorescent in situ hybridization (FISH) was used to detect specific groups of bacteria such as the alpha,beta,gamma-subdivisions of Proteobacteria, Gram-positive bacteria with a high G + C DNA content, Planctomycetes, Betaproteobacterial ammonia-oxidizing bacteria and nitrifying bacteria. The presence of the herbicide and/or urea affected the bacterial community structure, showing that FISH is a valuable tool for determining the response of bacterial populations to different environmental conditions. Copyright 2005 Society of Chemical Industry

Long-term starvation and subsequent recovery of nitrifiers in aerated submerged fixed-bed biofilm reactors.

PubMed

Elawwad, Abdelsalam; Sandner, Hendrik; Kappelmeyer, Uwe; Koeser, Heinz

2013-01-01

The effectiveness of three operational strategies for maintaining nitrifiers in bench-scale, aerated, submerged fixed-bed biofilm reactors (SFBBRs) during long-term starvation at 20 degrees C were evaluated. The operational strategies were characterized by the resulting oxidation-reduction potential (ORP) in the SFBBRs. The activity rates of the nitrifiers were measured and the activity decay was expressed by half-life times. It was found that anoxic and alternating anoxic/aerobic conditions were the best ways to preserve ammonia-oxidizing bacteria (AOB) during long starvation periods and resulted in half-life times of up to 34 and 28 days, respectively. Extended anaerobic conditions caused the half-life for AOB to decrease to 21 days. In comparison, the activity decay of nitrite-oxidizing bacteria (NOB) tended to be slightly faster. The activity of AOB biofilms that were kept for 97 days under anoxic conditions could be completely recovered in less than one week, while over 4 weeks was needed for AOB kept under anaerobic conditions. NOB were more sensitive to starvation and required longer recovery periods than AOB. For complete recovery, NOB needed approximately 7 weeks, regardless of the starvation conditions applied. Using the fluorescence in situ hybridization (FISH) technique, Nitrospira was detected as the dominant NOB genus. Among the AOB, the terminal restriction fragment length polymorphism (TRFLP) technique showed that during starvation and recovery periods, the relative frequency of species shifted to Nitrosomonas europaea/eutropha, regardless of the starvation condition. The consequences of these findings for the operation of SFBBRs under low-load and starvation conditions are discussed.

Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers

PubMed Central

Mußmann, Marc; Brito, Ivana; Pitcher, Angela; Sinninghe Damsté, Jaap S.; Hatzenpichler, Roland; Richter, Andreas; Nielsen, Jeppe L.; Nielsen, Per Halkjær; Müller, Anneliese; Daims, Holger; Wagner, Michael; Head, Ian M.

2011-01-01

Nitrification is a core process in the global nitrogen cycle that is essential for the functioning of many ecosystems. The discovery of autotrophic ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota has changed our perception of the microbiology of nitrification, in particular since their numerical dominance over ammonia-oxidizing bacteria (AOB) in many environments has been revealed. These and other data have led to a widely held assumption that all amoA-encoding members of the Thaumarchaeota (AEA) are autotrophic nitrifiers. In this study, 52 municipal and industrial wastewater treatment plants were screened for the presence of AEA and AOB. Thaumarchaeota carrying amoA were detected in high abundance only in four industrial plants. In one plant, thaumarchaeotes closely related to soil group I.1b outnumbered AOB up to 10,000-fold, and their numbers, which can only be explained by active growth in this continuous culture system, were two to three orders of magnitude higher than could be sustained by autotrophic ammonia oxidation. Consistently, 14CO2 fixation could only be detected in AOB but not in AEA in actively nitrifying sludge from this plant via FISH combined with microautoradiography. Furthermore, in situ transcription of archaeal amoA, and very weak in situ labeling of crenarchaeol after addition of 13CO2, was independent of the addition of ammonium. These data demonstrate that some amoA-carrying group I.1b Thaumarchaeota are not obligate chemolithoautotrophs. PMID:21930919

Detachment of solids and nitrifiers in integrated, fixed-film activated sludge systems.

PubMed

Maas, Carol L A; Parker, Wayne J; Legge, Raymond L

2008-12-01

Despite the importance of detachment to biofilm processes, detachment phenomena are not well understood. In this study, researchers investigated biofilm detachment from free-floating biofilm carriers that were established in an integrated, fixed-film activated sludge (IFAS) installation in Mississauga, Ontario. A method for assessing detachment from biofilm carrier systems was devised, evaluated, and refined during this study. In the absence of substrate, superficial air velocity significantly affected the 24-hour detachment rates of total suspended solids from the carriers. Short-term growth conditions did not appear to significantly affect the rate of detachment of solids and nitrifiers. The measured solids-detachment rates were found to be described by a second order function of biofilm attached growth total solids with a detachment coefficient of 0.006 +/- 0.0008 (g/m x d)(-1).

Conformation Change in a Self-recognizing Autotransporter Modulates Bacterial Cell-Cell Interaction*

PubMed Central

Girard, Victoria; Côté, Jean-Philippe; Charbonneau, Marie-Ève; Campos, Manuel; Berthiaume, Frédéric; Hancock, Mark A.; Siddiqui, Nadeem; Mourez, Michael

2010-01-01

Bacteria mostly live as multicellular communities, although they are unicellular organisms, yet the mechanisms that tie individual bacteria together are often poorly understood. The adhesin involved in diffuse adherence (AIDA-I) is an adhesin of diarrheagenic Escherichia coli strains. AIDA-I also mediates bacterial auto-aggregation and biofilm formation and thus could be important for the organization of communities of pathogens. Using purified protein and whole bacteria, we provide direct evidence that AIDA-I promotes auto-aggregation by interacting with itself. Using various biophysical and biochemical techniques, we observed a conformational change in the protein during AIDA-AIDA interactions, strengthening the notion that this is a highly specific interaction. The self-association of AIDA-I is of high affinity but can be modulated by sodium chloride. We observe that a bile salt, sodium deoxycholate, also prevents AIDA-I oligomerization and bacterial auto-aggregation. Thus, we propose that AIDA-I, and most likely other similar autotransporters such as antigen 43 (Ag43) and TibA, organize bacterial communities of pathogens through a self-recognition mechanism that is sensitive to the environment. This could permit bacteria to switch between multicellular and unicellular lifestyles to complete their infection. PMID:20123991

Development of Novel Random Network Theory-Based Approaches to Identify Network Interactions among Nitrifying Bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Cindy

2015-07-17

The interactions among different microbial populations in a community could play more important roles in determining ecosystem functioning than species numbers and their abundances, but very little is known about such network interactions at a community level. The goal of this project is to develop novel framework approaches and associated software tools to characterize the network interactions in microbial communities based on high throughput, large scale high-throughput metagenomics data and apply these approaches to understand the impacts of environmental changes (e.g., climate change, contamination) on network interactions among different nitrifying populations and associated microbial communities.

Integration of Vibrio vulnificus into Marine Aggregates and Its Subsequent Uptake by Crassostrea virginica Oysters

PubMed Central

Froelich, Brett; Ayrapetyan, Mesrop

2013-01-01

Marine aggregates are naturally forming conglomerations of larvacean houses, phytoplankton, microbes, and inorganics adhered together by exocellular polymers. In this study, we show in vitro that the bacterial pathogen Vibrio vulnificus can be concentrated into laboratory-generated aggregates from surrounding water. We further show that environmental (E-genotype) strains exhibit significantly more integration into these aggregates than clinical (C-genotype) strains. Experiments where marine aggregates with attached V. vulnificus cells were fed to oysters (Crassostrea virginica) resulted in greater uptake of both C and E types than nonaggregated controls. When C- and E-genotype strains were cocultured in competitive experiments, the aggregated E-genotype strains exhibited significantly greater uptake by oyster than the C-genotype strains. PMID:23263962

Seasonal-related effects on ammonium removal in activated carbon filter biologically enhanced by heterotrophic nitrifying bacteria for drinking water treatment.

PubMed

Qin, Wen; Li, Wei-Guang; Gong, Xu-Jin; Huang, Xiao-Fei; Fan, Wen-Biao; Zhang, Duoying; Yao, Peng; Wang, Xiao-Ju; Song, Yang

2017-08-01

To determine the potential effects of seasonal changes on water temperature and water quality upon removal of ammonium and organic carbon pollutants and to characterize the variations in microbial characteristics, a pilot-scale activated carbon filter biologically enhanced with heterotrophic nitrifying bacteria was investigated for 528 days. The results show that 69.2 ± 28.6% of ammonium and 23.1 ± 11.6% of the dissolved organic carbon were removed by the biologically enhanced activated carbon (BEAC) reactor. It is shown that higher biodegradable dissolved organic carbon enhances ammonium removal, even at low temperatures. The C/N ratio consumed by the BEAC reactor reached a steady value (i.e., 3.3) after 2 months of operation. Despite seasonal fluctuations and competition of the indigenous community, the heterotrophic nitrifying bacteria (Acinetobacter sp. HRBLi 16 and Acinetobacter harbinensis strain HITLi 7) remained relatively stable. The amount of carbon source was the most significant environmental parameter and dramatically affected the microbial community compositions in the BEAC reactor. The present study provides new insights into the application of a BEAC reactor for ammonium removal from drinking water, resisting strong seasonal changes.

Extracellular Polymeric Substance Production and Aggregated Bacteria Colonization Influence the Competition of Microbes in Biofilms.

PubMed

Jayathilake, Pahala G; Jana, Saikat; Rushton, Steve; Swailes, David; Bridgens, Ben; Curtis, Tom; Chen, Jinju

2017-01-01

The production of extracellular polymeric substance (EPS) is important for the survival of biofilms. However, EPS production is costly for bacteria and the bacterial strains that produce EPS (EPS+) grow in the same environment as non-producers (EPS-) leading to competition between these strains for nutrients and space. The outcome of this competition is likely to be dependent on factors such as initial attachment, EPS production rate, ambient nutrient levels and quorum sensing. We use an Individual-based Model (IbM) to study the competition between EPS+ and EPS- strains by varying the nature of initial colonizers which can either be in the form of single cells or multicellular aggregates. The microbes with EPS+ characteristics obtain a competitive advantage if they initially colonize the surface as smaller aggregates and are widely spread-out between the cells of EPS-, when both are deposited on the substratum. Furthermore, the results show that quorum sensing-regulated EPS production may significantly reduce the fitness of EPS producers when they initially deposit as aggregates. The results provide insights into how the distribution of bacterial aggregates during initial colonization could be a deciding factor in the competition among different strains in biofilms.

Bacterial interactions in dental biofilm development.

PubMed

Hojo, K; Nagaoka, S; Ohshima, T; Maeda, N

2009-11-01

Recent analyses with ribosomal RNA-based technologies have revealed the diversity of bacterial populations within dental biofilms, and have highlighted their important contributions to oral health and disease. Dental biofilms are exceedingly complex and multispecies ecosystems, where oral bacteria interact cooperatively or competitively with other members. Bacterial interactions that influence dental biofilm communities include various different mechanisms. During the early stage of biofilm formation, it is known that planktonic bacterial cells directly attach to surfaces of the oral cavity or indirectly bind to other bacterial cells that have already colonized. Adherence through co-aggregation may be critical for the temporary retention of bacteria on dental surfaces, and may facilitate eventual bacterial colonization. It is likely that metabolic communication, genetic exchange, production of inhibitory factors (e.g., bacteriocins, hydrogen peroxide, etc.), and quorum-sensing are pivotal regulatory factors that determine the bacterial composition and/or metabolism. Since each bacterium can easily access a neighboring bacterial cell and its metabolites, genetic exchanges and metabolic communication may occur frequently in dental biofilms. Quorum-sensing is defined as gene regulation in response to cell density, which influences various functions, e.g., virulence and bacteriocin production. In this review, we discuss these important interactions among oral bacteria within the dental biofilm communities.

Particle Aggregation During Fe(III) Bioreduction in Nontronite

NASA Astrophysics Data System (ADS)

Jaisi, D. P.; Dong, H.; Hi, Z.; Kim, J.

2005-12-01

This study was performed to evaluate the rate and mechanism of particle aggregation during bacterial Fe (III) reduction in different size fractions of nontronite and to investigate the role of different factors contributing to particle aggregation. To achieve this goal, microbial Fe(III) reduction experiments were performed with lactate as an electron donor, Fe(III) in nontronite as an electron acceptor, and AQDS as an electron shuttle in bicarbonate buffer using Shewanella putrefaceins CN32. These experiments were performed with and without Na- pyrophosphate as a dispersant in four size fractions of nontronite (0.12-0.22, 0.41-0.69, 0.73-0.96 and 1.42-1.8 mm). The rate of nontronite aggregation during the Fe(III) bioreduction was measured by analyzing particle size distribution using photon correlation spectroscopy (PCS) and SEM images analysis. Similarly, the changes in particle morphology during particle aggregation were determined by analyses of SEM images. Changes in particle surface charge were measured with electrophoretic mobility analyzer. The protein and carbohydrate fraction of EPS produced by cells during Fe(III) bioreduction was measured using Bradford and phenol-sulfuric acid extraction method, respectively. In the presence of the dispersant, the extent of Fe(III) bioreduction was 11.5-12.2% within the first 56 hours of the experiment. There was no measurable particle aggregation in control experiments. The PCS measurements showed that the increase in the effective diameter (95% percentile) was by a factor of 3.1 and 1.9 for particle size of 0.12-0.22 mm and 1.42-1.80 mm, respectively. The SEM image analyses also gave the similar magnitude of increase in particle size. In the absence of the dispersant, the extent of Fe(III) bioreduction was 13.4-14.5% in 56 hours of the experiment. The rate of aggregation was higher than that in the presence of the dispersant. The increase in the effective diameter (95% percentile) was by a factor of 13.6 and 4.1 for

Microbial Ecology of Soil Aggregation in Agroecosystems

NASA Astrophysics Data System (ADS)

Hofmockel, K. S.; Bell, S.; Tfailly, M.; Thompson, A.; Callister, S.

2017-12-01

Crop selection and soil texture influence the physicochemical attributes of the soil, which structures microbial communities and influences soil C cycling storage. At the molecular scale, microbial metabolites and necromass alter the soil environment, which creates feedbacks that influence ecosystem functions, including soil C accumulation. By integrating lab to field studies we aim to identify the molecules, organisms and metabolic pathways that control carbon cycling and stabilization in bioenergy soils. We investigated the relative influence of plants, microbes, and minerals on soil aggregate ecology at the Great Lakes Bioenergy Research experiment. Sites in WI and MI, USA have been in corn and switchgrass cropping systems for a decade. By comparing soil aggregate ecology across sites and cropping systems we are able to test the relative importance of plant, microbe, mineral influences on soil aggregate dynamics. Soil microbial communities (16S) differ in diversity and phylogeny among sites and cropping systems. FT-ICR MS revealed differences in the molecular composition of water-soluble fraction of soil organic matter for cropping systems and soil origin for both relative abundance of assigned formulas and biogeochemical classes of compounds. We found the degree of aggregation, measured by mean weighted diameter of aggregate fractions, is influenced by plant-soil interactions. Similarly, the proportion of soil aggregate fractions varied by both soil and plant factors. Differences in aggregation were reflected in differences in bacterial, but not fungal community composition across aggregate fractions, within each soil. Scanning electron microscopy revealed stark differences in mineral-organic interactions that influence the microbial niche and the accessibility of substrates within the soil. The clay soils show greater surface heterogeneity, enabling interactions with organic fraction of the soil. This is consistent with molecular data that reveal differences

Bacterial Inclusion Bodies Contain Amyloid-Like Structure

PubMed Central

Wang, Lei; Maji, Samir K; Sawaya, Michael R; Eisenberg, David; Riek, Roland

2008-01-01

Protein aggregation is a process in which identical proteins self-associate into imperfectly ordered macroscopic entities. Such aggregates are generally classified as amorphous, lacking any long-range order, or highly ordered fibrils. Protein fibrils can be composed of native globular molecules, such as the hemoglobin molecules in sickle-cell fibrils, or can be reorganized β-sheet–rich aggregates, termed amyloid-like fibrils. Amyloid fibrils are associated with several pathological conditions in humans, including Alzheimer disease and diabetes type II. We studied the structure of bacterial inclusion bodies, which have been believed to belong to the amorphous class of aggregates. We demonstrate that all three in vivo-derived inclusion bodies studied are amyloid-like and comprised of amino-acid sequence-specific cross-β structure. These findings suggest that inclusion bodies are structured, that amyloid formation is an omnipresent process both in eukaryotes and prokaryotes, and that amino acid sequences evolve to avoid the amyloid conformation. PMID:18684013

Population Structure of Manganese-Oxidizing Bacteria in Stratified Soils and Properties of Manganese Oxide Aggregates under Manganese–Complex Medium Enrichment

PubMed Central

Zhang, Zhongming; Chen, Hong; Liu, Jin; Ali, Muhammad; Liu, Fan; Li, Lin

2013-01-01

Manganese-oxidizing bacteria in the aquatic environment have been comprehensively investigated. However, little information is available about the distribution and biogeochemical significance of these bacteria in terrestrial soil environments. In this study, stratified soils were initially examined to investigate the community structure and diversity of manganese-oxidizing bacteria. Total 344 culturable bacterial isolates from all substrata exhibited Mn(II)-oxidizing activities at the range of 1 µM to 240 µM of the equivalent MnO2. The high Mn(II)-oxidizing isolates (>50 mM MnO2) were identified as the species of phyla Actinobacteria, Firmicutes and Proteobacteria. Seven novel Mn(II)-oxidizing bacterial genera (species), namely, Escherichia, Agromyces, Cellulomonas, Cupriavidus, Microbacterium, Ralstonia, and Variovorax, were revealed via comparative phylogenetic analysis. Moreover, an increase in the diversity of soil bacterial community was observed after the combined enrichment of Mn(II) and carbon-rich complex. The phylogenetic classification of the enriched bacteria represented by predominant denaturing gradient gel electrophoresis bands, was apparently similar to culturable Mn(II)-oxidizing bacteria. The experiments were further undertaken to investigate the properties of the Mn oxide aggregates formed by the bacterial isolates with high Mn(II)-oxidizing activity. Results showed that these bacteria were closely encrusted with their Mn oxides and formed regular microspherical aggregates under prolonged Mn(II) and carbon-rich medium enrichment for three weeks. The biotic oxidation of Mn(II) to Mn(III/IV) by these isolates was confirmed by kinetic examinations. X-ray diffraction assays showed the characteristic peaks of several Mn oxides and rhodochrosite from these aggregates. Leucoberbelin blue tests also verified the Mn(II)-oxidizing activity of these aggregates. These results demonstrated that Mn oxides were formed at certain amounts under the enrichment

Mineral trioxide aggregate: part 2 - a review of the material aspects.

PubMed

Malhotra, Neeraj; Agarwal, Antara; Mala, Kundabala

2013-03-01

The purpose of this two-part series is to review the composition, properties, and products of mineral trioxide aggregate (MTA) materials. PubMed and MedLine electronic databases were used to identify scientific papers from January 1991 to May 2010. Based on the selected inclusion criteria, citations were referenced from the scientific peer-reviewed dental literature. Mineral trioxide aggregate is a refined form of the parent compound, Portland cement (PC), and demonstrates a strong biocompatibility due to the high pH level and the material's ability to form hydroxyapatite. Mineral trioxide aggregate materials provide better microleakage protection than traditional endodontic materials as observed in findings from dye-leakage, fluid-filtration, protein-leakage, and bacterial penetration-leakage studies and has been recognized as a bioactive material. Various MTA commercial products are available, including gray mineral trioxide aggregate (GMTA), white mineral trioxide aggregate (WMTA), and mineral trioxide aggregate-Angelus (AMTA). Although these materials are indicated for various dental uses and applications, long-term in-vivo clinical studies are needed. Part 1 of this article highlighted and discussed the composition and characteristics of the material. Part 2 provides an overview of commercially available MTA materials.

The antigen 43 structure reveals a molecular Velcro-like mechanism of autotransporter-mediated bacterial clumping

PubMed Central

Heras, Begoña; Totsika, Makrina; Peters, Kate M.; Paxman, Jason J.; Gee, Christine L.; Jarrott, Russell J.; Perugini, Matthew A.; Whitten, Andrew E.; Schembri, Mark A.

2014-01-01

Aggregation and biofilm formation are critical mechanisms for bacterial resistance to host immune factors and antibiotics. Autotransporter (AT) proteins, which represent the largest group of outer-membrane and secreted proteins in Gram-negative bacteria, contribute significantly to these phenotypes. Despite their abundance and role in bacterial pathogenesis, most AT proteins have not been structurally characterized, and there is a paucity of detailed information with regard to their mode of action. Here we report the structure–function relationships of Antigen 43 (Ag43a), a prototypic self-associating AT protein from uropathogenic Escherichia coli. The functional domain of Ag43a displays a twisted L-shaped β-helical structure firmly stabilized by a 3D hydrogen-bonded scaffold. Notably, the distinctive Ag43a L shape facilitates self-association and cell aggregation. Combining all our data, we define a molecular “Velcro-like” mechanism of AT-mediated bacterial clumping, which can be tailored to fit different bacterial lifestyles such as the formation of biofilms. PMID:24335802

Morphomechanics of bacterial biofilms undergoing anisotropic differential growth

NASA Astrophysics Data System (ADS)

Zhang, Cheng; Li, Bo; Huang, Xiao; Ni, Yong; Feng, Xi-Qiao

2016-10-01

Growing bacterial biofilms exhibit a number of surface morphologies, e.g., concentric wrinkles, radial ridges, and labyrinthine networks, depending on their physiological status and nutrient access. We explore the mechanisms underlying the emergence of these greatly different morphologies. Ginzburg-Landau kinetic method and Fourier spectral method are integrated to simulate the morphological evolution of bacterial biofilms. It is shown that the morphological instability of biofilms is triggered by the stresses induced by anisotropic and heterogeneous bacterial expansion, and involves the competition between membrane energy and bending energy. Local interfacial delamination further enriches the morphologies of biofilms. Phase diagrams are established to reveal how the anisotropy and spatial heterogeneity of growth modulate the surface patterns. The mechanics of three-dimensional microbial morphogenesis may also underpin self-organization in other development systems and provide a potential strategy for engineering microscopic structures from bacterial aggregates.

Modification of nitrifying biofilm into nitritating one by combination of increased free ammonia concentrations, lowered HRT and dissolved oxygen concentration.

PubMed

Zekker, Ivar; Rikmann, Ergo; Tenno, Toomas; Menert, Anne; Lemmiksoo, Vallo; Saluste, Alar; Tenno, Taavo; Tomingas, Martin

2011-01-01

Nitrifying biomass on ring-shaped carriers was modified to nitritating one in a relatively short period of time (37 days) by limiting the air supply, changing the aeration regime, shortening the hydraulic retention time and increasing free ammonia (FA) concentration in the moving-bed biofilm reactor (MBBR). The most efficient strategy for the development and maintenance of nitritating biofilm was found to be the inhibition of nitrifying activity by higher FA concentrations (up to 6.5 mg/L) in the process. Reject water from sludge treatment from the Tallinn Wastewater Treatment Plant was used as substrate in the MBBR. The performance of high-surfaced biocarriers taken from the nitritating activity MBBR was further studied in batch tests to investigate nitritation and nitrification kinetics with various FA concentrations and temperatures. The maximum nitrite accumulation ratio (96.6%) expressed as the percentage of NO2(-)-N/NOx(-)-N was achieved for FA concentration of 70 mg/L at 36 degrees C. Under the same conditions the specific nitrite oxidation rate achieved was 30 times lower than the specific nitrite formation rate. It was demonstrated that in the biofilm system, inhibition by FA combined with the optimization of the main control parameters is a good strategy to achieve nitritating activity and suppress nitrification.

[Effects of selective microbial inhibitors on the microbial transformation of phosphorous in aggregates of highly weathered red soil with rice straw amendment].

PubMed

Ding, Long-jun; Xiao, He-ai; Wu, Jin-shui; Ge, Ti-da

2010-07-01

In order to further understand the mechanisms of microbial immobilization of phosphorous (P) in highly weathered red soil with organic amendment, an incubation test was conducted to investigate the roles of microbial functional groups in the transformation of P in 0.2-2 mm soil aggregates. Throughout the 90-day incubation period, amendment with rice straw induced a substantial increase in the amounts of microbial biomass C and P, Olsen-P, and organic P in the aggregates. Comparing with rice straw amendment alone, the amendment with rice straw plus fungal inhibitor actidione decreased the amount of microbial biomass C in the aggregates by 10.5%-31.8% in the first 30 days. Such a decrement was significantly larger than that (6.8%-11.6%) in the treatment amended with rice straw plus bacterial inhibitors tetracycline and streptomycin sulphate (P<0.01). After the first 30 days, the microbial biomass C remained constant. In the first 20 days, the amount of microbial biomass P in the aggregates was 10.0%-28.8% higher in the treatment amended with bacterial inhibitors than in the treatment amended with fungal inhibitor (P<0.01). All the results suggested that that both the fungal and the bacterial groups were involved in the microbial immobilization of P in the soil aggregates, and the fungal group played a relatively larger role.

Protein corona between nanoparticles and bacterial proteins in activated sludge: Characterization and effect on nanoparticle aggregation.

PubMed

Zhang, Peng; Xu, Xiao-Yan; Chen, You-Peng; Xiao, Meng-Qian; Feng, Bo; Tian, Kai-Xun; Chen, Yue-Hui; Dai, You-Zhi

2018-02-01

In this work, the protein coronas of activated sludge proteins on TiO 2 nanoparticles (TNPs) and ZnO nanoparticles (ZNPs) were characterized. The proteins with high affinity to TNPs and ZNPs were identified by shotgun proteomics, and their effects of on the distributions of TNPs and ZNPs in activated sludge were concluded. In addition, the effects of protein coronas on the aggregations of TNPs and ZNPs were evaluated. Thirty and nine proteins with high affinities to TNPs and ZNPs were identified, respectively. The proteomics and adsorption isotherms demonstrated that activated sludge had a higher affinity to TNPs than to ZNPs. The aggregation percentages of ZNPs at 35, 53, and 106 mg/L of proteins were 13%, 14%, and 18%, respectively, whereas those of TNPs were 21%, 30%, 41%, respectively. The proteins contributed to ZNPs aggregation by dissolved Zn ion-bridging, whereas the increasing protein concentrations enhanced the TNPs aggregation through macromolecule bridging flocculation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Removal of micropollutants during tertiary wastewater treatment by biofiltration: Role of nitrifiers and removal mechanisms.

PubMed

Rattier, M; Reungoat, J; Keller, J; Gernjak, W

2014-05-01

The objective of this study was to determine the extent to which a suite of organic micropollutants (MPs) can be removed by biological filtration and the role of bioavailability and ammonia oxidizing microorganisms (AOMs) in the biodegradation process. During approximately one year, laboratory-scale columns with 8 min empty bed contact time (EBCT) and packed with anthracite as filter media were used for treating a tertiary effluent spiked with a broad range of MPs at a target concentration of 2 μg L(-1). In parallel columns, aerobic biomass growth was inhibited by using either the biocide sodium azide (500 mg L(-1) NaN3) or allylthiourea (5 mg L(-1) ATU), specifically inhibiting nitrifying bacteria. Once the biomass had colonized the media, around 15% of the dissolved organic carbon (DOC) contained in the untreated tertiary effluent was removed by non-inhibited columns. The removal of several MPs increased over time indicating the relevance of biological activity for the removal of MPs, while the negative control, the NaN3 inhibited column, showed no significant removal. Out of 33 MPs, 19 were recalcitrant (<25%) to biodegradation under aerobic conditions with the others exhibiting a diverse range of removal efficiency up to 95%. Through inhibition by ATU it was shown that nitrifying bacteria were clearly having a role in the degradation of several MPs, whereas the removal of other MPs was not affected by the presence of the nitrification inhibitor. A relationship between the qualitative assessment of sorption of MPs on granular activated carbon (GAC) and their removal efficiency by biodegradation on anthracite was observed. This result suggested that the affinity of the MPs for GAC media could be a useful indicator of the bioavailability of compounds during biofiltration on anthracite. Copyright © 2014 Elsevier Ltd. All rights reserved.

Isolation of cell-free bacterial inclusion bodies.

PubMed

Rodríguez-Carmona, Escarlata; Cano-Garrido, Olivia; Seras-Franzoso, Joaquin; Villaverde, Antonio; García-Fruitós, Elena

2010-09-17

Bacterial inclusion bodies are submicron protein clusters usually found in recombinant bacteria that have been traditionally considered as undesirable products from protein production processes. However, being fully biocompatible, they have been recently characterized as nanoparticulate inert materials useful as scaffolds for tissue engineering, with potentially wider applicability in biomedicine and material sciences. Current protocols for inclusion body isolation from Escherichia coli usually offer between 95 to 99% of protein recovery, what in practical terms, might imply extensive bacterial cell contamination, not compatible with the use of inclusion bodies in biological interfaces. Using an appropriate combination of chemical and mechanical cell disruption methods we have established a convenient procedure for the recovery of bacterial inclusion bodies with undetectable levels of viable cell contamination, below 10⁻¹ cfu/ml, keeping the particulate organization of these aggregates regarding size and protein folding features. The application of the developed protocol allows obtaining bacterial free inclusion bodies suitable for use in mammalian cell cultures and other biological interfaces.

Rapid Aggregation of Biofuel-Producing Algae by the Bacterium Bacillus sp. Strain RP1137

PubMed Central

Powell, Ryan J.

2013-01-01

Algal biofuels represent one of the most promising means of sustainably replacing liquid fuels. However, significant challenges remain before alga-based fuels become competitive with fossil fuels. One of the largest challenges is the ability to harvest the algae in an economical and low-energy manner. In this article, we describe the isolation of a bacterial strain, Bacillus sp. strain RP1137, which can rapidly aggregate several algae that are candidates for biofuel production, including a Nannochloropsis sp. This bacterium aggregates algae in a pH-dependent and reversible manner and retains its aggregation ability after paraformaldehyde fixation, opening the possibility for reuse of the cells. The optimal ratio of bacteria to algae is described, as is the robustness of aggregation at different salinities and temperatures. Aggregation is dependent on the presence of calcium or magnesium ions. The efficiency of aggregation of Nannochloropsis oceanica IMET1 is between 70 and 95% and is comparable to that obtained by other means of harvest; however, the rate of harvest is fast, with aggregates forming in 30 s. PMID:23892750

The Physics of Amyloid Aggregation and Templating in Prions

NASA Astrophysics Data System (ADS)

Cox, Daniel

2012-02-01

The problem of self-assembled amyloid aggregation of proteins in structures with beta-strands perpendicular to a one dimensional grown axis is interesting at a fundamental level (is this the most generic end state of proteins?), from a biological level (if the self-assembly can be regulated it is of use in contexts like spider silk and bacterial colony formation), for human public health (aggregation unregulated induces diseases like mad cow and Alzheimer's), and for possible materials applications (e.g., in tissue scaffolding). In this presentation, I will review the work of my group in examining the possibility that the left-handed beta helix (LHBH) structure can be the building block of the aggregates of mammalian prion and yeast prion proteins. I will also discuss our efforts to assess the possibility of a novel pH driven structural switch between LHBH and alpha-helical forms in the ordered half of the mammalian prion protein, and now the possibly pH stabilized LHBH structure can template aggregate growth of the disordered half of the protein, identified in numerous experimental studies as most relevant to disease.

Performance and bacterial community structure of a 10-years old constructed mangrove wetland.

PubMed

Tian, Tingting; Tam, Nora F Y; Zan, Qijie; Cheung, S G; Shin, Paul K S; Wong, Y S; Zhang, Li; Chen, Zhanghe

2017-11-30

Constructed mangrove wetland has been used for wastewater treatment but its long-term performance has not been reported. One-year monitoring of a 10-years old horizontal subsurface-flow constructed mangrove wetland consisting of three belts, two with mangrove plants and one without, revealed that the system maintained high and stable removal percentages of organic matter and nutrients, and planted belts performed better than unplanted control. Substrates in belts planted with Aegiceras corniculatum or Kandelia obovata had higher abundance of ammonifiers, nitrifiers and denitrifiers but lower total heterotrophic bacteria than unplanted substrate. Denaturing gradient gel electrophoresis showed that microbial diversity in planted substrate was significantly lower than that in unplanted one. The bacteria in substrates, irrespective to belts, were phylogenetically related to Proteobacteria (most dominant), Acidobacteria, Firmicutes, Nitrospirae, Gemmatimonadetes, Chloroflexi and Cyanobacteria. The steady performance of this 10-year old constructed mangrove wetland was affected by the abundance and diversity of bacterial community in substrate. Copyright © 2017 Elsevier Ltd. All rights reserved.

The response of aggregated Pseudomonas putida CP1 cells to UV-C and UV-A/B disinfection.

PubMed

Maganha de Almeida, Ana C; Quilty, Bríd

2016-11-01

UV radiation is a spread method used worldwide for the disinfection of water. However, much of the research on the disinfection of bacterial cells by UV has focused on planktonic cells. Many bacterial cells in nature are present in clumps or aggregates, and these aggregates, which are more resistant to disinfection than their planktonic counterparts, can be problematic in engineered water systems. The current research used Pseudomonas putida (P. putida) CP1, an environmental and non-pathogenic microorganism which autoaggregates when grown under certain conditions, as a model organism to simulate aggregated cells. The study investigated the response of both the planktonic and the aggregated forms of the bacterium to UV-C (λ = 253.7 nm) and UV-A/B (λ > 300 nm) disinfection at laboratory scale in a minimal medium. The planktonic cells of P. putida CP1 were inactivated within 60 s by UV-C and in 60 min by UV-A/B; however, the aggregated cells required 120 min of UV-C treatment and 240 min of UV-A/B radiation to become inactive. The size of the aggregate was reduced following UV treatment. Although all the cells had lost culturability, viability as measured by the LIVE/DEAD ® stain and epifluorescence microscopy was not completely lost and the cells all demonstrated regrowth after overnight incubation in the dark.

Effect of copper treatment on the composition and function of the bacterial community in the sponge Haliclona cymaeformis.

PubMed

Tian, Ren-Mao; Wang, Yong; Bougouffa, Salim; Gao, Zhao-Ming; Cai, Lin; Zhang, Wei-Peng; Bajic, Vladimir; Qian, Pei-Yuan

2014-11-04

Marine sponges are the most primitive metazoan and host symbiotic microorganisms. They are crucial components of the marine ecological system and play an essential role in pelagic processes. Copper pollution is currently a widespread problem and poses a threat to marine organisms. Here, we examined the effects of copper treatment on the composition of the sponge-associated bacterial community and the genetic features that facilitate the survival of enriched bacteria under copper stress. The 16S rRNA gene sequencing results showed that the sponge Haliclona cymaeformis harbored symbiotic sulfur-oxidizing Ectothiorhodospiraceae and photosynthetic Cyanobacteria as dominant species. However, these autotrophic bacteria decreased substantially after treatment with a high copper concentration, which enriched for a heterotrophic-bacterium-dominated community. Metagenomic comparison revealed a varied profile of functional genes and enriched functions, including bacterial motility and chemotaxis, extracellular polysaccharide and capsule synthesis, virulence-associated genes, and genes involved in cell signaling and regulation, suggesting short-period mechanisms of the enriched bacterial community for surviving copper stress in the microenvironment of the sponge. Microscopic observation and comparison revealed dynamic bacterial aggregation within the matrix and lysis of sponge cells. The bacteriophage community was also enriched, and the complete genome of a dominant phage was determined, implying that a lytic phage cycle was stimulated by the high copper concentration. This study demonstrated a copper-induced shift in the composition of functional genes of the sponge-associated bacterial community, revealing the selective effect of copper treatment on the functions of the bacterial community in the microenvironment of the sponge. This study determined the bacterial community structure of the common sponge Haliclona cymaeformis and examined the effect of copper treatment on

Bacterial entombment by intratubular mineralization following orthograde mineral trioxide aggregate obturation: a scanning electron microscopy study

PubMed Central

Yoo, Jun Sang; Chang, Seok-Woo; Oh, So Ram; Perinpanayagam, Hiran; Lim, Sang-Min; Yoo, Yeon-Jee; Oh, Yeo-Rok; Woo, Sang-Bin; Han, Seung-Hyun; Zhu, Qiang; Kum, Kee-Yeon

2014-01-01

The time domain entombment of bacteria by intratubular mineralization following orthograde canal obturation with mineral trioxide aggregate (MTA) was studied by scanning electron microscopy (SEM). Single-rooted human premolars (n=60) were instrumented to an apical size #50/0.06 using ProFile and treated as follows: Group 1 (n=10) was filled with phosphate buffered saline (PBS); Group 2 (n=10) was incubated with Enterococcus faecalis for 3 weeks, and then filled with PBS; Group 3 (n=20) was obturated orthograde with a paste of OrthoMTA (BioMTA, Seoul, Korea) and PBS; and Group 4 (n=20) was incubated with E. faecalis for 3 weeks and then obturated with OrthoMTA–PBS paste. Following their treatments, the coronal openings were sealed with PBS-soaked cotton and intermediate restorative material (IRM), and the roots were then stored in PBS for 1, 2, 4, 8 or 16 weeks. After each incubation period, the roots were split and their dentin/MTA interfaces examined in both longitudinal and horizontal directions by SEM. There appeared to be an increase in intratubular mineralization over time in the OrthoMTA-filled roots (Groups 3 and 4). Furthermore, there was a gradual entombment of bacteria within the dentinal tubules in the E. faecalis inoculated MTA-filled roots (Group 4). Therefore, the orthograde obturation of root canals with OrthoMTA mixed with PBS may create a favorable environment for bacterial entombment by intratubular mineralization. PMID:25012869

Microbiological parameters of aggregates in typical chernozems of long-term field experiments

NASA Astrophysics Data System (ADS)

Zhelezova, A. D.; Tkhakakhova, A. K.; Yaroslavtseva, N. V.; Garbuz, S. A.; Lazarev, V. I.; Kogut, B. M.; Kutovaya, O. V.; Kholodov, V. A.

2017-06-01

The changes in microbiological parameters of aggregates (1-2 mm) in typical chernozems under different land uses as dependent on the intensity and character of anthropogenic loads were studied with the help of the real-time polymerase chain reaction (PCR). The samples from the following long-term field experiments were examined: permanent black fallow, continuous cultivation of potato, 17-year-old unmanaged fallow after permanent black fallow, and annually mown reserved steppe. The soil samples were treated in two ways. In the first case, the samples were air-dried, sieved through the screens to separate aggregate fraction of 1-2 mm, and microbiological parameters were determined in this fraction. In the second case, the samples were frozen immediately after the sampling, and the aggregates of 1-2 mm were manually separated from the samples before the PCR analysis. It was shown that air-dry aggregates of chernozems could be used for the quantitative analysis of DNA of microbial community in comparative studies. According to the quantitative estimate of the content of DNA fragments from different phylogenetic groups, the bacterial community was most sensitive to the type of the soil use, and its restoration after the removal of extreme anthropogenic loads proceeded faster than that of other microorganisms. The content of archaeal DNA in the chernozem under the 17-year-old unmanaged fallow did not differ significantly from its content in the annually plowed chernozems. The changes in the content of micromycetal DNA related to anthropogenic load decrease were intermediate between changes in the contents of archaeal and bacterial DNA.

Effect of free ammonia concentration on monochloramine penetration within a nitrifying biofilm and its effect on activity, viability, and recovery.

PubMed

Pressman, Jonathan G; Lee, Woo Hyoung; Bishop, Paul L; Wahman, David G

2012-03-01

Chloramine has replaced free chorine for secondary disinfection at many water utilities because of disinfection by-product (DBP) regulations. Because chloramination provides a source of ammonia, there is a potential for nitrification when using chloramines. Nitrification in drinking water distribution systems is undesirable and may result in degradation of water quality and subsequent non-compliance with existing regulations. Thus, nitrification control is a major issue and likely to become increasingly important as chloramine use increases. In this study, monochloramine penetration and its effect on nitrifying biofilm activity, viability, and recovery was investigated and evaluated using microelectrodes and confocal laser scanning microscopy (CLSM). Monochloramine was applied to nitrifying biofilm for 24 h at two different chlorine to nitrogen (Cl(2):N) mass ratios (4:1 [4.4 mg Cl(2)/L] or 1:1 Cl(2):N [5.3 mg Cl(2)/L]), resulting in either a low (0.23 mg N/L) or high (4.2 mg N/L) free ammonia concentration. Subsequently, these biofilm samples were allowed to recover without monochloramine and receiving 4.2 mg N/L free ammonia. Under both monochloramine application conditions, monochloramine fully penetrated into the nitrifying biofilm within 24 h. Despite this complete monochloramine penetration, complete viability loss did not occur, and both biofilm samples subsequently recovered aerobic activity when fed only free ammonia. When monochloramine was applied with a low free ammonia concentration, dissolved oxygen (DO) fully penetrated, but with a high free ammonia concentration, complete cessation of aerobic activity (i.e., oxygen utilization) did not occur and subsequent analysis indicated that oxygen consumption still remained near the substratum. During the ammonia only recovery phase, different spatial recoveries were seen in each of the samples, based on oxygen utilization. It appears that the presence of higher free ammonia concentration allowed a

Platelet Activation by Streptococcus pyogenes Leads to Entrapment in Platelet Aggregates, from Which Bacteria Subsequently Escape

PubMed Central

Svensson, Lisbeth; Baumgarten, Maria; Mörgelin, Matthias

2014-01-01

Platelet activation and aggregation have been reported to occur in response to a number of Gram-positive pathogens. Here, we show that platelet aggregates induced by Streptococcus pyogenes were unstable and that viable bacteria escaped from the aggregates over time. This was not due to differential activation in response to the bacteria compared with physiological activators. All the bacterial isolates induced significant platelet activation, including integrin activation and alpha and dense-granule release, at levels equivalent to those induced by potent physiological platelet activators that induced stable aggregates. The ability to escape the aggregates and to resist the antibacterial effects of platelets was dependent on active protein synthesis by the bacteria within the aggregate. We conclude that S. pyogenes bacteria can temporarily cover themselves with activated platelets, and we propose that this may facilitate survival of the bacteria in the presence of platelets. PMID:25069984

Bacterial community analysis of an industrial wastewater treatment plant in Colombia with screening for lipid-degrading microorganisms.

PubMed

Silva-Bedoya, Lina Marcela; Sánchez-Pinzón, María Solange; Cadavid-Restrepo, Gloria Ester; Moreno-Herrera, Claudia Ximena

2016-11-01

The operation of wastewater treatment technologies depends on a combination of physical, chemical and biological factors. Microorganisms present in wastewater treatment plants play essential roles in the degradation and removal of organic waste and xenobiotic pollutants. Several microorganisms have been used in complementary treatments to process effluents rich in fats and oils. Microbial lipases have received significant industrial attention because of their stability, broad substrate specificity, high yields, and regular supply, as well as the fact that the microorganisms producing them grow rapidly on inexpensive media. In Colombia, bacterial community studies have focused on populations of cultivable nitrifying, heterotrophic and nitrogen-fixing bacteria present in constructed wetlands. In this study, culture-dependent methods, culture-independent methods (TTGE, RISA) and enzymatic methods were used to estimate bacterial diversity, to monitor temporal and spatial changes in bacterial communities, and to screen microorganisms that presented lipolytic activity. The dominant microorganisms in the Wastewater Treatment Plant (WWTP) examined in this study belonged to the phyla Firmicutes, Proteobacteria and Bacteroidetes. The enzymatic studies performed indicated that five bacterial isolates and three fungal isolates possessed the ability to degrade lipids; additionally, the Serratia, Kosakonia and Mucor genera presented lipase-mediated transesterification activity. The implications of these findings in regard to possible applications are discussed later in this paper. Our results indicate that there is a wide diversity of aerobic Gram-negative bacteria inhabiting the different sections of the WWTP, which could indicate its ecological condition, functioning and general efficiency. Copyright © 2016 Elsevier GmbH. All rights reserved.

Kinetics of bacterial phospholipase C activity at micellar interfaces: effect of substrate aggregate microstructure and a model for the kinetic parameters.

PubMed

Singh, Jasmeet; Ranganathan, Radha; Hajdu, Joseph

2008-12-25

Activity at micellar interfaces of bacterial phospholipase C from Bacillus cereus on phospholipids solubilized in micelles was investigated with the goal of elucidating the role of the interface microstructure and developing further an existing kinetic model. Enzyme kinetics and physicochemical characterization of model substrate aggregates were combined, thus enabling the interpretation of kinetics in the context of the interface. Substrates were diacylphosphatidylcholine of different acyl chain lengths in the form of mixed micelles with dodecyldimethylammoniopropanesulfonate. An early kinetic model, reformulated to reflect the interfacial nature of the kinetics, was applied to the kinetic data. A better method of data treatment is proposed, use of which makes the presence of microstructure effects quite transparent. Models for enzyme-micelle binding and enzyme-lipid binding are developed, and expressions incorporating the microstructural properties are derived for the enzyme-micelle dissociation constant K(s) and the interface Michaelis-Menten constant, K(M). Use of these expressions in the interface kinetic model brings excellent agreement between the kinetic data and the model. Numerical values for the thermodynamic and kinetic parameters are determined. Enzyme-lipid binding is found to be an activated process with an acyl chain length dependent free energy of activation that decreases with micelle lipid molar fraction with a coefficient of about -15RT and correlates with the tightness of molecular packing in the substrate aggregate. Thus, the physical insight obtained includes a model for the kinetic parameters that shows that these parameters depend on the substrate concentration and acyl chain length of the lipid. Enzyme-micelle binding is indicated to be hydrophobic and solvent mediated with a dissociation constant of 1.2 mM.

Office of Naval Research Aggregate Dynamics in the Sea Workshop Held at Pacific Grove, California on September 22-24, 1986

DTIC Science & Technology

1986-09-01

collision, etc.) originate from largely biogenically derived component particles. Local loss terms include sinking, advection and decomposition which...Some quarry or scrape away the aggregate surface, others consume entire particles. Bacterial decomposition on the particle surfaces may also weaken...major role in the degradation of aggregates. Only limited information is available regarding microbial colonization, hydrolysis , and metabolism of the

Fitness and Recovery of Bacterial Communities and Antibiotic Resistance Genes in Urban Wastewaters Exposed to Classical Disinfection Treatments.

PubMed

Di Cesare, Andrea; Fontaneto, Diego; Doppelbauer, Julia; Corno, Gianluca

2016-09-20

Antibiotic resistance genes (ARGs) are increasingly appreciated to be important as micropollutants. Indirectly produced by human activities, they are released into the environment, as they are untargeted by conventional wastewater treatments. In order to understand the fate of ARGs and of other resistant forms (e.g., phenotypical adaptations) in urban wastewater treatment plants (WWTPs), we monitored three WWTPs with different disinfection processes (chlorine, peracetic acid (PAA), and ultraviolet light (UV)). We monitored WWTPs influx and pre- and postdisinfection effluent over 24 h, followed by incubation experiments lasting for 96 h. We measured bacterial abundance, size distribution and aggregational behavior, the proportion of intact (active) cells, and the abundances of four ARGs and of the mobile element integron1. While all the predisinfection treatments of all WWTPs removed the majority of bacteria and of associated ARGs, of the disinfection processes only PAA efficiently removed bacterial cells. However, the stress imposed by PAA selected for bacterial aggregates and, similarly to chlorine, stimulated the selection of ARGs during the incubation experiment. This suggests disinfections based on chemically aggressive destruction of bacterial cell structures can promote a residual microbial community that is more resistant to antibiotics and, given the altered aggregational behavior, to competitive stress in nature.

Synchrotron-based micro and nanotomographic investigations of soil aggregate microbial and pore structure

NASA Astrophysics Data System (ADS)

Kemner, K. M.; O'Brien, S.; Whiteside, M. D.; Sholto-Douglas, D.; Antipova, O.; Bailey, V.; Boyanov, M.; Dohnalkova, A.; Gursoy, D.; Kovarik, L.; Lai, B.; Roehrig, C.; Vogt, S.

2017-12-01

Soil is a highly complex network of pore spaces, minerals, and organic matter (e.g., roots, fungi, and bacteria), making it physically heterogeneous over nano- to macro-scales. Such complexity arises from feedbacks between physical processes and biological activity that generate a dynamic, self-organizing 3D complex. Since we first demonstrated the utility of synchrotron-based transmission tomography to image internal soil aggregate structure [Kemner et al., 1998], we and many other researchers have made use of and have advanced the application of this technique. However, our understanding of how microbes and microbial metabolism are distributed throughout soil aggregates is limited, because no technique is available to image the soil pore network and the life that inhabits it. X-ray transmission microtomography can provide highly detailed 3D renderings of soil structure but cannot distinguish cells from other electron-light material such as air or water. However, the use of CdSe quantum dots (QDs) as a reporter of bacterial presence enables us to overcome this constraint, instilling bacterial cells with enough contrast to detect them and their metabolic functions in their opaque soil habitat, with hard x-rays capable of penetrating 3D soil structures at high resolution. Previous transmission tomographic imaging of soil aggregates with high energy synchrotron x-rays has demonstrated 700 nm3 voxel spatial resolution. These and recent results from nanotomographic x-ray transmission imaging of soil aggregates with 30 nm3 voxel resolution will be presented. In addition, results of submicron voxel-sized x-ray fluorescence 3D imaging to determine microbial distributions within soil aggregates and the critical role to be played by the upgrade of the Advanced Photon Source for 100-1000X increases in hard x-ray brilliance will also be presented. *Kemner, et al., SPIE 3449, 45-53, 1998

ActA Promotes Listeria monocytogenes Aggregation, Intestinal Colonization and Carriage

PubMed Central

Travier, Laetitia; Guadagnini, Stéphanie; Gouin, Edith; Dufour, Alexandre; Chenal-Francisque, Viviane; Cossart, Pascale; Olivo-Marin, Jean-Christophe; Ghigo, Jean-Marc; Disson, Olivier; Lecuit, Marc

2013-01-01

Listeria monocytogenes (Lm) is a ubiquitous bacterium able to survive and thrive within the environment and readily colonizes a wide range of substrates, often as a biofilm. It is also a facultative intracellular pathogen, which actively invades diverse hosts and induces listeriosis. So far, these two complementary facets of Lm biology have been studied independently. Here we demonstrate that the major Lm virulence determinant ActA, a PrfA-regulated gene product enabling actin polymerization and thereby promoting its intracellular motility and cell-to-cell spread, is critical for bacterial aggregation and biofilm formation. We show that ActA mediates Lm aggregation via direct ActA-ActA interactions and that the ActA C-terminal region, which is not involved in actin polymerization, is essential for aggregation in vitro. In mice permissive to orally-acquired listeriosis, ActA-mediated Lm aggregation is not observed in infected tissues but occurs in the gut lumen. Strikingly, ActA-dependent aggregating bacteria exhibit an increased ability to persist within the cecum and colon lumen of mice, and are shed in the feces three order of magnitude more efficiently and for twice as long than bacteria unable to aggregate. In conclusion, this study identifies a novel function for ActA and illustrates that in addition to contributing to its dissemination within the host, ActA plays a key role in Lm persistence within the host and in transmission from the host back to the environment. PMID:23382675

Ecosystem Resilience and Limitations Revealed by Soil Bacterial Community Dynamics in a Bark Beetle-Impacted Forest

PubMed Central

Brouillard, Brent M.; Bokman, Chelsea M.; Sharp, Jonathan O.

2017-01-01

ABSTRACT Forested ecosystems throughout the world are experiencing increases in the incidence and magnitude of insect-induced tree mortality with large ecologic ramifications. Interestingly, correlations between water quality and the extent of tree mortality in Colorado montane ecosystems suggest compensatory effects from adjacent live vegetation that mute responses in less severely impacted forests. To this end, we investigated whether the composition of the soil bacterial community and associated functionality beneath beetle-killed lodgepole pine was influenced by the extent of surrounding tree mortality. The most pronounced changes were observed in the potentially active bacterial community, where alpha diversity increased in concert with surrounding tree mortality until mortality exceeded a tipping point of ~30 to 40%, after which diversity stabilized and decreased. Community structure also clustered in association with the extent of surrounding tree mortality with compositional trends best explained by differences in NH4+ concentrations and C/N ratios. C/N ratios, which were lower in soils under beetle-killed trees, further correlated with the relative abundance of putative nitrifiers and exoenzyme activity. Collectively, the response of soil microorganisms that drive heterotrophic respiration and decay supports observations of broader macroscale threshold effects on water quality in heavily infested forests and could be utilized as a predictive mechanism during analogous ecosystem disruptions. PMID:29208740

Role of the disaggregase ClpB in processing of proteins aggregated as inclusion bodies.

PubMed

Zblewska, Kamila; Krajewska, Joanna; Zolkiewski, Michal; Kędzierska-Mieszkowska, Sabina

2014-08-01

Overproduction of heterologous proteins in bacterial systems often results in the formation of insoluble inclusion bodies (IBs), which is a major impediment in biochemical research and biotechnology. In principle, the activity of molecular chaperones could be employed to gain control over the IB formation and to improve the recombinant protein yields, but the potential of each of the major bacterial chaperones (DnaK/J, GroEL/ES, and ClpB) to process IBs has not been fully established yet. We investigated the formation of inclusion bodies (IBs) of two aggregation-prone proteins, VP1LAC and VP1GFP, overproduced in Escherichiacoli in the presence and absence of the chaperone ClpB. We found that both ClpB isoforms, ClpB95 and ClpB80 accumulated in E. coli cells during the production of IBs. The amount of IB proteins increased in the absence of ClpB. ClpB supported the resolubilization and reactivation of the aggregated VP1LAC and VP1GFP in E. coli cells. The IB disaggregation was optimal in the presence of both ClpB95 and ClpB80. Our results indicate an essential role of ClpB in controlling protein aggregation and inclusion body formation in bacteria. Copyright © 2014 Elsevier Inc. All rights reserved.

Effect of saliva viscosity on the co-aggregation between oral streptococci and Actinomyces naeslundii.

PubMed

Kitada, Katsuhiro; Oho, Takahiko

2012-06-01

The co-aggregation of oral bacteria leads to their clearance from the oral cavity. Poor oral hygiene and high saliva viscosity are common amongst the elderly; thus, they frequently suffer from pneumonia caused by the aspiration of oral microorganisms. To examine the direct effect of saliva viscosity on the co-aggregation of oral streptococci with actinomyces. Fifteen oral streptococcal and a single actinomyces strain were used. Co-aggregation was assessed by a visual assay in phosphate buffer and a spectrophotometric assay in the same buffer containing 0-60% glycerol or whole saliva. Nine oral streptococci co-aggregated with Actinomyces naeslundii ATCC12104 in the visual assay and were subsequently used for the spectrophotometric analysis. All tested strains displayed a decrease in co-aggregation with increasing amounts of glycerol in the buffer. The co-aggregation of Streptococcus oralis with A. naeslundii recovered to baseline level following the removal of glycerol. The per cent co-aggregation of S. oralis with A. naeslundii was significantly correlated with the viscosity in unstimulated and stimulated whole saliva samples (correlation coefficients: -0.52 and -0.48, respectively). This study suggests that saliva viscosity affects the co-aggregation of oral streptococci with actinomyces and that bacterial co-aggregation decreases with increasing saliva viscosity. © 2011 The Gerodontology Society and John Wiley & Sons A/S.

Bacterially mediated mineralization of vaterite

NASA Astrophysics Data System (ADS)

Rodriguez-Navarro, Carlos; Jimenez-Lopez, Concepcion; Rodriguez-Navarro, Alejandro; Gonzalez-Muñoz, Maria Teresa; Rodriguez-Gallego, Manuel

2007-03-01

Myxococcus xanthus, a common soil bacterium, plays an active role in the formation of spheroidal vaterite. Bacterial production of CO 2 and NH 3 and the transformation of the NH 3 to NH4+ and OH -, thus increasing solution pH and carbonate alkalinity, set the physicochemical conditions (high supersaturation) leading to vaterite precipitation in the microenvironment around cells, and directly onto the surface of bacterial cells. In the latter case, fossilization of bacteria occurs. Vaterite crystals formed by aggregation of oriented nanocrystals with c-axis normal to the bacterial cell-wall, or to the core of the spherulite when bacteria were not encapsulated. While preferred orientation of vaterite c-axis appears to be determined by electrostatic affinity (ionotropic effect) between vaterite crystal (0001) planes and the negatively charged functional groups of organic molecules on the bacterium cell-wall or on extracellular polymeric substances (EPS), analysis of the changes in the culture medium chemistry as well as high resolution transmission electron microscopy (HRTEM) observations point to polymorph selection by physicochemical (kinetic) factors (high supersaturation) and stabilization by organics, both connected with bacterial activity. The latter is in agreement with inorganic precipitation of vaterite induced by NH 3 and CO 2 addition in the protein-rich sterile culture medium. Our results as well as recent studies on vaterite precipitation in the presence of different types of bacteria suggest that bacterially mediated vaterite precipitation is not strain-specific, and could be more common than previously thought.

Learning about protein solubility from bacterial inclusion bodies

PubMed Central

Martínez-Alonso, Mónica; González-Montalbán, Nuria; García-Fruitós, Elena; Villaverde, Antonio

2009-01-01

The progressive solving of the conformation of aggregated proteins and the conceptual understanding of the biology of inclusion bodies in recombinant bacteria is providing exciting insights on protein folding and quality. Interestingly, newest data also show an unexpected functional and structural complexity of soluble recombinant protein species and picture the whole bacterial cell factory scenario as more intricate than formerly believed. PMID:19133126

Free-living bacterial communities associated with tubeworm (Ridgeia piscesae) aggregations in contrasting diffuse flow hydrothermal vent habitats at the Main Endeavour Field, Juan de Fuca Ridge

PubMed Central

Forget, Nathalie L; Kim Juniper, S

2013-01-01

We systematically studied free-living bacterial diversity within aggregations of the vestimentiferan tubeworm Ridgeia piscesae sampled from two contrasting flow regimes (High Flow and Low Flow) in the Endeavour Hydrothermal Vents Marine Protected Area (MPA) on the Juan de Fuca Ridge (Northeast Pacific). Eight samples of particulate detritus were recovered from paired tubeworm grabs from four vent sites. Most sequences (454 tag and Sanger methods) were affiliated to the Epsilonproteobacteria, and the sulfur-oxidizing genus Sulfurovum was dominant in all samples. Gammaproteobacteria were also detected, mainly in Low Flow sequence libraries, and were affiliated with known methanotrophs and decomposers. The cooccurrence of sulfur reducers from the Deltaproteobacteria and the Epsilonproteobacteria suggests internal sulfur cycling within these habitats. Other phyla detected included Bacteroidetes, Actinobacteria, Chloroflexi, Firmicutes, Planctomycetes, Verrucomicrobia, and Deinococcus–Thermus. Statistically significant relationships between sequence library composition and habitat type suggest a predictable pattern for High Flow and Low Flow environments. Most sequences significantly more represented in High Flow libraries were related to sulfur and hydrogen oxidizers, while mainly heterotrophic groups were more represented in Low Flow libraries. Differences in temperature, available energy for metabolism, and stability between High Flow and Low Flow habitats potentially explain their distinct bacterial communities. PMID:23401293

A paradigm shift towards low-nitrifying production systems: the role of biological nitrification inhibition (BNI).

PubMed

Subbarao, G V; Sahrawat, K L; Nakahara, K; Rao, I M; Ishitani, M; Hash, C T; Kishii, M; Bonnett, D G; Berry, W L; Lata, J C

2013-07-01

Agriculture is the single largest geo-engineering initiative that humans have initiated on planet Earth, largely through the introduction of unprecedented amounts of reactive nitrogen (N) into ecosystems. A major portion of this reactive N applied as fertilizer leaks into the environment in massive amounts, with cascading negative effects on ecosystem health and function. Natural ecosystems utilize many of the multiple pathways in the N cycle to regulate N flow. In contrast, the massive amounts of N currently applied to agricultural systems cycle primarily through the nitrification pathway, a single inefficient route that channels much of this reactive N into the environment. This is largely due to the rapid nitrifying soil environment of present-day agricultural systems. In this Viewpoint paper, the importance of regulating nitrification as a strategy to minimize N leakage and to improve N-use efficiency (NUE) in agricultural systems is highlighted. The ability to suppress soil nitrification by the release of nitrification inhibitors from plant roots is termed 'biological nitrification inhibition' (BNI), an active plant-mediated natural function that can limit the amount of N cycling via the nitrification pathway. The development of a bioassay using luminescent Nitrosomonas to quantify nitrification inhibitory activity from roots has facilitated the characterization of BNI function. Release of BNIs from roots is a tightly regulated physiological process, with extensive genetic variability found in selected crops and pasture grasses. Here, the current status of understanding of the BNI function is reviewed using Brachiaria forage grasses, wheat and sorghum to illustrate how BNI function can be utilized for achieving low-nitrifying agricultural systems. A fundamental shift towards ammonium (NH4(+))-dominated agricultural systems could be achieved by using crops and pastures with high BNI capacities. When viewed from an agricultural and environmental perspective, the

A paradigm shift towards low-nitrifying production systems: the role of biological nitrification inhibition (BNI)

PubMed Central

Subbarao, G. V.; Sahrawat, K. L.; Nakahara, K.; Rao, I. M.; Ishitani, M.; Hash, C. T.; Kishii, M.; Bonnett, D. G.; Berry, W. L.; Lata, J. C.

2013-01-01

Background Agriculture is the single largest geo-engineering initiative that humans have initiated on planet Earth, largely through the introduction of unprecedented amounts of reactive nitrogen (N) into ecosystems. A major portion of this reactive N applied as fertilizer leaks into the environment in massive amounts, with cascading negative effects on ecosystem health and function. Natural ecosystems utilize many of the multiple pathways in the N cycle to regulate N flow. In contrast, the massive amounts of N currently applied to agricultural systems cycle primarily through the nitrification pathway, a single inefficient route that channels much of this reactive N into the environment. This is largely due to the rapid nitrifying soil environment of present-day agricultural systems. Scope In this Viewpoint paper, the importance of regulating nitrification as a strategy to minimize N leakage and to improve N-use efficiency (NUE) in agricultural systems is highlighted. The ability to suppress soil nitrification by the release of nitrification inhibitors from plant roots is termed ‘biological nitrification inhibition’ (BNI), an active plant-mediated natural function that can limit the amount of N cycling via the nitrification pathway. The development of a bioassay using luminescent Nitrosomonas to quantify nitrification inhibitory activity from roots has facilitated the characterization of BNI function. Release of BNIs from roots is a tightly regulated physiological process, with extensive genetic variability found in selected crops and pasture grasses. Here, the current status of understanding of the BNI function is reviewed using Brachiaria forage grasses, wheat and sorghum to illustrate how BNI function can be utilized for achieving low-nitrifying agricultural systems. A fundamental shift towards ammonium (NH4+)-dominated agricultural systems could be achieved by using crops and pastures with high BNI capacities. When viewed from an agricultural and

Nitrous oxide production and mRNA expression analysis of nitrifying and denitrifying bacterial genes under floodwater disappearance and fertilizer application.

PubMed

Riya, Shohei; Takeuchi, Yuki; Zhou, Sheng; Terada, Akihiko; Hosomi, Masaaki

2017-06-01

A pulse of nitrous oxide (N 2 O) emission has been observed following the disappearance of floodwater by drainage. However, its mechanism is not well understood. We conducted a column study to clarify the mechanism for N 2 O production during floodwater disappearance by using a microsensor and determining the bacterial gene expression. An increase in N 2 O flux was observed following floodwater disappearance after the addition of NH 4 + , with a corresponding increase in the concentrations of NO 3 - and dissolved N 2 O in the oxic and anoxic soil layers, respectively. The transcription level of the bacterial amoA mRNA did not change, while that of nirK mRNA increased sharply after an hour of floodwater disappearance. An additional anoxic soil slurry experiment demonstrated that the addition of NO 3 - induced the expression of nirK gene and caused a concomitant increase in N 2 O production. These findings suggest that NO 3 - production in the oxic layers is important as it provides a substrate and induces the synthesis of denitrification enzymes in the anoxic layer during N 2 O production.

Effect of nitrification inhibitor DMPP on nitrogen leaching, nitrifying organisms, and enzyme activities in a rice-oilseed rape cropping system.

PubMed

Li, Hua; Liang, Xinqiang; Chen, Yingxu; Lian, Yanfeng; Tian, Guangming; Ni, Wuzhong

2008-01-01

DMPP (3,4-dimethylpyrazole phosphate) has been used to reduce nitrogen (N) loss from leaching or denitrification and to improve N supply in agricultural land. However, its impact on soil nitrifying organisms and enzyme activities involved in N cycling is largely unknown. Therefore, an on-farm experiment, for two years, has been conducted, to elucidate the effects of DMPP on mineral N (NH4(+)-N and NO3(-)-N) leaching, nitrifying organisms, and denitrifying enzymes in a rice-oilseed rape cropping system. Three treatments including urea alone (UA), urea + 1% DMPP (DP), and no fertilizer (CK), have been carried out. The results showed that DP enhanced the mean NH4(+)-N concentrations by 19.1%--24.3%, but reduced the mean NO3(-)-N concentrations by 44.9%--56.6% in the leachate, under a two-year rice-rape rotation, compared to the UA treatment. The population of ammonia oxidizing bacteria, the activity of nitrate reductase, and nitrite reductase in the DP treatment decreased about 24.5%--30.9%, 14.9%--43.5%, and 14.7%--31.6%, respectively, as compared to the UA treatment. However, nitrite oxidizing bacteria and hydroxylamine reductase remained almost unaffected by DMPP. It is proposed that DMPP has the potential to either reduce NO3(-)-N leaching by inhibiting ammonia oxidization or N losses from denitrification, which is in favor of the N conversations in the rice-oilseed rape cropping system.

Thermal Aggregation of Calcium-Fortified Skim Milk Enhances Probiotic Protection during Convective Droplet Drying.

PubMed

Wang, Juan; Huang, Song; Fu, Nan; Jeantet, Romain; Chen, Xiao Dong

2016-08-03

Probiotic bacteria have been reported to confer benefits on hosts when delivered in an adequate dose. Spray-drying is expected to produce dried and microencapsulated probiotic products due to its low production cost and high energy efficiency. The bottleneck in probiotic application addresses the thermal and dehydration-related inactivation of bacteria during process. A protective drying matrix was designed by modifying skim milk with the principle of calcium-induced protein thermal aggregation. The well-defined single-droplet drying technique was used to monitor the droplet-particle conversion and the protective effect of this modified Ca-aggregated milk on Lactobacillus rhamnosus GG. The Ca-aggregated milk exhibited a higher drying efficiency and superior protection on L. rhamnosus GG during thermal convective drying. The mechanism was explained by the aggregation in milk, causing the lower binding of water in the serum phase and, conversely, local concentrated milk aggregates involved in bacteria entrapment in the course of drying. This work may open new avenues for the development of probiotic products with high bacterial viability and calcium enrichment.

Inhabitancy of active Nitrosopumilus-like ammonia-oxidizing archaea and Nitrospira nitrite-oxidizing bacteria in the sponge Theonella swinhoei

PubMed Central

Feng, Guofang; Sun, Wei; Zhang, Fengli; Karthik, Loganathan; Li, Zhiyong

2016-01-01

Nitrification directly contributes to the ammonia removal in sponges, and it plays an indispensable role in sponge-mediated nitrogen cycle. Previous studies have demonstrated genomic evidences of nitrifying lineages in the sponge Theonella swinhoei. However, little is known about the transcriptional activity of nitrifying community in this sponge. In this study, combined DNA- and transcript-based analyses were performed to reveal the composition and transcriptional activity of the nitrifiers in T. swinhoei from the South China Sea. Transcriptional activity of ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in this sponge were confirmed by targeting their nitrifying genes,16S rRNA genes and their transcripts. Phylogenetic analysis coupled with RDP rRNA classification indicated that archaeal 16S rRNA genes, amoA (the subunit of ammonia monooxygenase) genes and their transcripts were closely related to Nitrosopumilus-like AOA; whereas nitrifying bacterial 16S rRNA genes, nxrB (the subunit of nitrite oxidoreductase) genes and their transcripts were closely related to Nitrospira NOB. Quantitative assessment demonstrated relative higher abundances of nitrifying genes and transcripts of Nitrosopumilus-like AOA than those of Nitrospira NOB in this sponge. This study illustrated the transcriptional potentials of Nitrosopumilus-like archaea and Nitrospira bacteria that would predominantly contribute to the nitrification functionality in the South China Sea T. swinhoei. PMID:27113140

Initial and hourly headloss modelling on a tertiary nitrifying wastewater biofiltration plant.

PubMed

Bernier, Jean; Rocher, Vincent; Lessard, Paul

2016-01-01

The headloss prediction capability of a wastewater biofiltration model is evaluated on data from a full-scale tertiary nitrifying biofilter unit located in the Paris conurbation (Achères, France; 6,000,000 population equivalent). The model has been previously calibrated on nutrient conversion and TSS filtration observations. In this paper the mass of extracted biofilm during biofilter backwash and the headloss value at the start of an operation cycle are first calibrated on sludge production estimations and relative pressure measurements over the year 2009. The calibrated model is then used on two one-month periods in 2012 for which hourly headloss measurements were acquired. The observed trends are correctly predicted for 2009 but the model exhibits some heavy daily variation that is not found in measurements. Hourly predictions stay close to observations, although the model error rises slightly when the headloss does not vary much. The global model shows that both nutrient conversion and headloss build-up can be reasonably well predicted at the same time on a full-scale plant.

Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest

PubMed Central

Rasche, Frank; Knapp, Daniela; Kaiser, Christina; Koranda, Marianne; Kitzler, Barbara; Zechmeister-Boltenstern, Sophie; Richter, Andreas; Sessitsch, Angela

2011-01-01

It was hypothesized that seasonality and resource availability altered through tree girdling were major determinants of the phylogenetic composition of the archaeal and bacterial community in a temperate beech forest soil. During a 2-year field experiment, involving girdling of beech trees to intercept the transfer of easily available carbon (C) from the canopy to roots, members of the dominant phylogenetic microbial phyla residing in top soils under girdled versus untreated control trees were monitored at bimonthly intervals through 16S rRNA gene-based terminal restriction fragment length polymorphism profiling and quantitative PCR analysis. Effects on nitrifying and denitrifying groups were assessed by measuring the abundances of nirS and nosZ genes as well as bacterial and archaeal amoA genes. Seasonal dynamics displayed by key phylogenetic and nitrogen (N) cycling functional groups were found to be tightly coupled with seasonal alterations in labile C and N pools as well as with variation in soil temperature and soil moisture. In particular, archaea and acidobacteria were highly responsive to soil nutritional and soil climatic changes associated with seasonality, indicating their high metabolic versatility and capability to adapt to environmental changes. For these phyla, significant interrelations with soil chemical and microbial process data were found suggesting their potential, but poorly described contribution to nitrification or denitrification in temperate forest soils. In conclusion, our extensive approach allowed us to get novel insights into effects of seasonality and resource availability on the microbial community, in particular on hitherto poorly studied bacterial phyla and functional groups. PMID:20882059

Postfragmentation density function for bacterial aggregates in laminar flow.

PubMed

Byrne, Erin; Dzul, Steve; Solomon, Michael; Younger, John; Bortz, David M

2011-04-01

The postfragmentation probability density of daughter flocs is one of the least well-understood aspects of modeling flocculation. We use three-dimensional positional data of Klebsiella pneumoniae bacterial flocs in suspension and the knowledge of hydrodynamic properties of a laminar flow field to construct a probability density function of floc volumes after a fragmentation event. We provide computational results which predict that the primary fragmentation mechanism for large flocs is erosion. The postfragmentation probability density function has a strong dependence on the size of the original floc and indicates that most fragmentation events result in clumps of one to three bacteria eroding from the original floc. We also provide numerical evidence that exhaustive fragmentation yields a limiting density inconsistent with the log-normal density predicted in the literature, most likely due to the heterogeneous nature of K. pneumoniae flocs. To support our conclusions, artificial flocs were generated and display similar postfragmentation density and exhaustive fragmentation. ©2011 American Physical Society

Postfragmentation density function for bacterial aggregates in laminar flow

PubMed Central

Byrne, Erin; Dzul, Steve; Solomon, Michael; Younger, John

2014-01-01

The postfragmentation probability density of daughter flocs is one of the least well-understood aspects of modeling flocculation. We use three-dimensional positional data of Klebsiella pneumoniae bacterial flocs in suspension and the knowledge of hydrodynamic properties of a laminar flow field to construct a probability density function of floc volumes after a fragmentation event. We provide computational results which predict that the primary fragmentation mechanism for large flocs is erosion. The postfragmentation probability density function has a strong dependence on the size of the original floc and indicates that most fragmentation events result in clumps of one to three bacteria eroding from the original floc. We also provide numerical evidence that exhaustive fragmentation yields a limiting density inconsistent with the log-normal density predicted in the literature, most likely due to the heterogeneous nature of K. pneumoniae flocs. To support our conclusions, artificial flocs were generated and display similar postfragmentation density and exhaustive fragmentation. PMID:21599205

Nitrification and Autotrophic Nitrifying Bacteria in a Hydrocarbon-Polluted Soil

PubMed Central

Deni, Jamal; Penninckx, Michel J.

1999-01-01

In vitro ammonia-oxidizing bacteria are capable of oxidizing hydrocarbons incompletely. This transformation is accompanied by competitive inhibition of ammonia monooxygenase, the first key enzyme in nitrification. The effect of hydrocarbon pollution on soil nitrification was examined in situ. In a microcosm study, adding diesel fuel hydrocarbon to an uncontaminated soil (agricultural unfertilized soil) treated with ammonium sulfate dramatically reduced the amount of KCl-extractable nitrate but stimulated ammonium consumption. In a soil with long history of pollution that was treated with ammonium sulfate, 90% of the ammonium was transformed into nitrate after 3 weeks of incubation. Nitrate production was twofold higher in the contaminated soil than in the agricultural soil to which hydrocarbon was not added. To assess if ammonia-oxidizing bacteria acquired resistance to inhibition by hydrocarbon, the contaminated soil was reexposed to diesel fuel. Ammonium consumption was not affected, but nitrate production was 30% lower than nitrate production in the absence of hydrocarbon. The apparent reduction in nitrification resulted from immobilization of ammonium by hydrocarbon-stimulated microbial activity. These results indicated that the hydrocarbon inhibited nitrification in the noncontaminated soil (agricultural soil) and that ammonia-oxidizing bacteria in the polluted soil acquired resistance to inhibition by the hydrocarbon, possibly by increasing the affinity of nitrifying bacteria for ammonium in the soil. PMID:10473409

Bacterial Inclusion Bodies: Discovering Their Better Half.

PubMed

Rinas, Ursula; Garcia-Fruitós, Elena; Corchero, José Luis; Vázquez, Esther; Seras-Franzoso, Joaquin; Villaverde, Antonio

2017-09-01

Bacterial inclusion bodies (IBs) are functional, non-toxic amyloids occurring in recombinant bacteria showing analogies with secretory granules of the mammalian endocrine system. The scientific interest in these mesoscale protein aggregates has been historically masked by their status as a hurdle in recombinant protein production. However, progressive understanding of how the cell handles the quality of recombinant polypeptides and the main features of their intriguing molecular organization has stimulated the interest in inclusion bodies and spurred their use in diverse technological fields. The engineering and tailoring of IBs as functional protein particles for materials science and biomedicine is a good example of how formerly undesired bacterial byproducts can be rediscovered as promising functional materials for a broad spectrum of applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

Solubilization of protein aggregates by the acid stress chaperones HdeA and HdeB.

PubMed

Malki, Abderrahim; Le, Hai-Tuong; Milles, Sigrid; Kern, Renée; Caldas, Teresa; Abdallah, Jad; Richarme, Gilbert

2008-05-16

The acid stress chaperones HdeA and HdeB of Escherichia coli prevent the aggregation of periplasmic proteins at acidic pH. We show in this report that they also form mixed aggregates with proteins that have failed to be solubilized at acidic pH and allow their subsequent solubilization at neutral pH. HdeA, HdeB, and HdeA and HdeB together display an increasing efficiency for the solubilization of protein aggregates at pH 3. They are less efficient for the solubilization of aggregates at pH 2, whereas HdeB is the most efficient. Increasing amounts of periplasmic proteins draw increasing amounts of chaperone into pellets, suggesting that chaperones co-aggregate with their substrate proteins. We observed a decrease in the size of protein aggregates in the presence of HdeA and HdeB, from very high molecular mass aggregates to 100-5000-kDa species. Moreover, a marked decrease in the exposed hydrophobicity of aggregated proteins in the presence of HdeA and HdeB was revealed by 1,1'-bis(4-anilino)naphtalene-5,5'-disulfonic acid binding experiments. In vivo, during the recovery at neutral pH of acid stressed bacterial cells, HdeA and HdeB allow the solubilization and renaturation of protein aggregates, including those formed by the maltose receptor MalE, the oligopeptide receptor OppA, and the histidine receptor HisJ. Thus, HdeA and HdeB not only help to maintain proteins in a soluble state during acid treatment, as previously reported, but also assist, both in vitro and in vivo, in the solubilization at neutral pH of mixed protein-chaperone aggregates formed at acidic pH, by decreasing the size of protein aggregates and the exposed hydrophobicity of aggregated proteins.

Removal of triclosan in nitrifying activated sludge: effects of ammonia amendment and bioaugmentation.

PubMed

Lee, Do Gyun; Cho, Kun-Ching; Chu, Kung-Hui

2015-04-01

This study investigated two possible strategies, increasing ammonia oxidation activity and bioaugmenting with triclosan-degrader Sphingopyxis strain KCY1, to enhance triclosan removal in nitrifying activated sludge (NAS). Triclosan (2 mg L(-1)) was removed within 96-h in NAS bioreactors amended with 5, 25 and 75 mg L(-1) of ammonium (NH4-N). The fastest triclosan removal was observed in 25 mg NH4-NL(-1) amended-bioreactors where high ammonia oxidation occurred. Inhibition of ammonia oxidation and slower triclosan removal were observed in 75 mg NH4-NL(-1) amended-bioreactors. Triclosan removal was correlated to the molar ratio of the amount of nitrate produced to the amount of ammonium removed. Bioaugmentation with strain KCY1 did not enhance triclosan removal in the bioreactors with active ammonia oxidation. Approximately 36-42% and 59% of triclosan added were removed within 24-h by ammonia-oxidizing bacteria and unknown triclosan-degrading heterotrophs, respectively. The results suggested that increasing ammonia oxidation activity can be an effective strategy to enhance triclosan removal in NAS. Copyright © 2015 Elsevier Ltd. All rights reserved.

N2O production by nitrifier denitrification in the Benguela Upwelling System

NASA Astrophysics Data System (ADS)

Frame, C. H.; Hou, L.; Lehmann, M. F.

2014-12-01

The Benguela upwelling system off the coast of southwestern Africa is an important zone of marine N2O production whose upwelling rates vary seasonally. Here we present N2O stable isotopic and isotopomeric data collected during a period of high upwelling (September 2013) and low upwelling (January 2014). During both periods, 15N-nitrite and 15N-ammonium tracer inucbation experiments were used to investigate N2O production by ammonia oxidizing microorganisms in the top 150m of the water column. N2O production from 15N-ammonium was not measurable during these incubations. However, we detected N2O production from 15N-nitrite, suggesting that nitrifier denitrification is a source of shallow N2O in this region. Furthermore, decreasing the pH of the incubation water enhanced the amount of N2O produced, suggesting that upwelling of CO2-rich/low-pH deep water may enhance N2O production in this region. Finally, we present our incubation data in the larger context of the N2O and nitrite isotopic and concentration profiles, with an eye toward comparing incubation-based N2O production rates with profile-based estimates.

A Consensus Method for the Prediction of ‘Aggregation-Prone’ Peptides in Globular Proteins

PubMed Central

Tsolis, Antonios C.; Papandreou, Nikos C.; Iconomidou, Vassiliki A.; Hamodrakas, Stavros J.

2013-01-01

The purpose of this work was to construct a consensus prediction algorithm of ‘aggregation-prone’ peptides in globular proteins, combining existing tools. This allows comparison of the different algorithms and the production of more objective and accurate results. Eleven (11) individual methods are combined and produce AMYLPRED2, a publicly, freely available web tool to academic users (http://biophysics.biol.uoa.gr/AMYLPRED2), for the consensus prediction of amyloidogenic determinants/‘aggregation-prone’ peptides in proteins, from sequence alone. The performance of AMYLPRED2 indicates that it functions better than individual aggregation-prediction algorithms, as perhaps expected. AMYLPRED2 is a useful tool for identifying amyloid-forming regions in proteins that are associated with several conformational diseases, called amyloidoses, such as Altzheimer's, Parkinson's, prion diseases and type II diabetes. It may also be useful for understanding the properties of protein folding and misfolding and for helping to the control of protein aggregation/solubility in biotechnology (recombinant proteins forming bacterial inclusion bodies) and biotherapeutics (monoclonal antibodies and biopharmaceutical proteins). PMID:23326595

Low temperature effects on nitrification and nitrifier community structure in V-ASP for decentralized wastewater treatment and its improvement by bio-augmentation.

PubMed

Yuan, Jiajia; Dong, Wenyi; Sun, Feiyun; Zhao, Ke

2018-03-01

The vegetation-activated sludge process (V-ASP) has been proved to be an environment-friendly decentralized wastewater treatment system with extra esthetic function and less footprint. However, the effects of low temperature on the treatment performance of V-ASP and related improvement methods are rarely investigated, up to now. In this work, the effect of low temperature on nitrification in V-ASP was comprehensively investigated from overall nitrification performance, substrate utilization kinetics, functional enzymatic activities, and microbial community structure shift by comparison with conventional ASP. Bio-augmentation methods in terms of single-time nitrifier-enriched biomass dosage were employed to improve nitrification efficiency in bench- and full-scale systems. The experiment results demonstrated that the NH 4 + -N removal efficiency in V-ASP system decreased when the operational temperature decreased from 30 to 15 °C, and the decreasing extent was rather smaller compared to ASP, as well as ammonium and nitrite oxidation rates and enzymatic activities, which indicated the V-ASP system possesses high resistance to low temperature. With direct dosage of 1.6 mg nitrifier/gSS sludge, the nitrification efficiency in V-ASP was enhanced dramatically from below 50% to above 90%, implying that bio-augmentation was effective for V-ASP whose enzymatic activities and microbial communities were both also improved. The feasibility and effectiveness of bio-augmentation was further confirmed in a full-scale V-ASP system after a long-term experiment which is instructive for the practical application.

Modeling FtsZ ring formation in the bacterial cell-anisotropic aggregation via mutual interactions of polymer rods.

PubMed

Fischer-Friedrich, Elisabeth; Gov, Nir

2011-04-01

The cytoskeletal protein FtsZ polymerizes to a ring structure (Z ring) at the inner cytoplasmic membrane that marks the future division site and scaffolds the division machinery in many bacterial species. FtsZ is known to polymerize in the presence of GTP into single-stranded protofilaments. In vivo, FtsZ polymers become associated with the cytoplasmic membrane via interaction with the membrane-binding proteins FtsA and ZipA. The FtsZ ring structure is highly dynamic and undergoes constantly polymerization and depolymerization processes and exchange with the cytoplasmic pool. In this theoretical study, we consider a scenario of Z ring self-organization via self-enhanced attachment of FtsZ polymers due to end-to-end interactions and lateral interactions of FtsZ polymers on the membrane. With the assumption of exclusively circumferential polymer orientations, we derive coarse-grained equations for the dynamics of the pool of cytoplasmic and membrane-bound FtsZ. To capture stochastic effects expected in the system due to low particle numbers, we simulate our computational model using a Gillespie-type algorithm. We obtain ring- and arc-shaped aggregations of FtsZ polymers on the membrane as a function of monomer numbers in the cell. In particular, our model predicts the number of FtsZ rings forming in the cell as a function of cell geometry and FtsZ concentration. We also calculate the time of FtsZ ring localization to the midplane in the presence of Min oscillations. Finally, we demonstrate that the assumptions and results of our model are confirmed by 3D reconstructions of fluorescently-labeled FtsZ structures in E. coli that we obtained.

Production of heterotrophic bacteria inhabiting macroscopic organic aggregates (marine snow) from surface waters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alldredge, A.L.; Cole, J.J.; Caron, D.A.

1986-01-01

Macroscopic detrital aggregates, known as marine snow, are a ubiquitous and abundant component of the marine pelagic zone. Descriptions of microbial communities occurring at densities 2-5 orders of magnitude higher on these particles than in the surrounding seawater have led to the suggestion that marine snow may be a site of intense heterotrophic activity. The authors tested this hypothesis using incorporation of (/sup 3/H)thymidine into macromolecules as a measure of bacterial growth occurring on marine snow from oceanic waters in the North Atlantic and from neritic waters off southern California. Abundances of marine snow ranged from 0.1 to 4.3 aggregatesmore » per liter. However, only 0.1-4% ration per cell on aggregates was generally equal to or lower than that of bacteria found free-living in the surrounding seawater, indicating that attached bacteria were not growing more rapidly than free-living bacteria. Bacteria inhabiting aggregates were up to 25 times larger than free-living forms.« less

Effects of graphite nanoparticles on nitrification in an activated sludge system.

PubMed

Dong, Qian; Liu, Yanchen; Shi, Hanchang; Huang, Xia

2017-09-01

Graphite nanoparticles (GNPs) might result in unexpected effects during their transportation and transformation in wastewater treatment systems, including strong thermo-catalytic and catalytic effects and microbial cytotoxicity. In particular, the effects of GNPs on the nitrification process in activated sludge systems should be addressed. This study aimed to estimate the influence of GNPs on the nitrification process in a short-term nitrification reactor with exposure to different light sources. The results indicated that GNPs could only improve the efficiency of photothermal transformation slightly in the activated sludge system because of its photothermal effects under the standard illuminant (imitating 1 × sun). However, even with better photothermal effects, the nitrification efficiency still decreased significantly with GNP dosing under the standard illuminant, which might result from stronger cytotoxic effects of GNPs on the nitrifying bacteria. The disappearance of extracellular polymeric substances (EPS) around bacterial cells was observed, and the total quantity of viable bacteria decreased significantly after GNP exposuring. Variation in bacterial groups primarily occurred in nitrifying microbial communities, including Nitrosomonas sp., Nitrosospira sp., Comamonas sp. and Bradyrhizobiace sp. Nitrifiers significantly decreased, while the phyla Gammaproteobacteria, Deinocccus, and Bacteroidetes exhibited greater stability during GNP treatment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Ammonia-oxidizing bacteria and archaea within biofilters of a commercial recirculating marine aquaculture system.

PubMed

Huang, Zhitao; Jiang, Yuli; Song, Xiefa; Hallerman, Eric; Peng, Lei; Dong, Dengpan; Ma, Teng; Zhai, Jieming; Li, Wensheng

2018-02-10

While biofilters are widely used to metabolize ammonia and other wastes in marine recirculating aquaculture systems, the ammonia-oxidizing bacterial and archaeal communities have not been characterized across a diversity of production systems. Using a metagenomics approach, we characterized the ammonia-oxidizing microbiological community of biofilters in a commercial recirculating marine aquaculture system producing hybrid grouper (Epinephelus lanceolatus × E. fuscoguttatus). Cloning and sequencing of the amoA gene showed that nitrifying bacteria included Nitrosomonas europea, N. stercoris, N. cryotolerans, N. eutropha, N. estuarii, eight strains of N. marina, and 15 strains not associated with described species. Nitrifying archaea included eight strains of Nitrosopumilus maritimus, N. koreensis, N. piranensis, N. adriaticus, undescribed congeners, and other undescribed archaea. The species composition of the bacterial and especially the archaeal communities was beyond that yet reported for aquaculture biofilters. While ammonia flux through the respective communities has yet to be estimated, the diverse environmental adaptations of the bacterial and archaeal communities suggest resilience of function under a range of environmental conditions.

Calcium oxalate monohydrate aggregation induced by aggregation of desialylated Tamm-Horsfall protein

PubMed Central

Viswanathan, Pragasam; Rimer, Jeffrey D.; Kolbach, Ann M.; Kleinman, Jack G.

2011-01-01

Tamm-Horsfall protein (THP) is thought to protect against calcium oxalate monohydrate (COM) stone formation by inhibiting COM aggregation. Several studies reported that stone formers produce THP with reduced levels of glycosylation, particularly sialic acid levels, which leads to reduced negative charge. In this study, normal THP was treated with neuraminidase to remove sialic acid residues, confirmed by an isoelectric point shift to higher pH. COM aggregation assays revealed that desialylated THP (ds-THP) promoted COM aggregation, while normal THP inhibited aggregation. The appearance of protein aggregates in solutions at ds-THP concentrations ≥1 µg/mL in 150 mM NaCl correlated with COM aggregation promotion, implying that ds-THP aggregation induced COM aggregation. The aggregation-promoting effect of the ds-THP was independent of pH above its isoelectric point, but was substantially reduced at low ionic strength, where protein aggregation was much reduced. COM aggregation promotion was maximized at a ds-THP to COM mass ratio of ~0.025, which can be explained by a model wherein partial COM surface coverage by ds-THP aggregates promotes crystal aggregation by bridging opposing COM surfaces, whereas higher surface coverage leads to repulsion between adsorbed ds-THP aggregates. Thus, desialylation of THP apparently abrogates a normal defensive action of THP by inducing protein aggregation, and subsequently COM aggregation, a condition that favors kidney stone formation. PMID:21229239

Impact of water quality on the bacterial populations and off-flavours in recirculating aquaculture systems.

PubMed

Auffret, Marc; Yergeau, Étienne; Pilote, Alexandre; Proulx, Émilie; Proulx, Daniel; Greer, Charles W; Vandenberg, Grant; Villemur, Richard

2013-05-01

A variety of factors affecting water quality in recirculating aquaculture systems (RAS) are associated with the occurrence of off-flavours. In this study, we report the impact of water quality on the bacterial diversity and the occurrence of the geosmin-synthesis gene (geoA) in two RAS units operated for 252 days. Unit 2 displayed a higher level of turbidity and phosphate, which affected the fresh water quality compared with unit 1. In the biofilter, nitrification is one of the major processes by which high water quality is maintained. The bacterial population observed in the unit 1 biofilter was more stable throughout the experiment, with a higher level of nitrifying bacteria compared with the unit 2 biofilter. Geosmin appeared in fish flesh after 84 days in unit 2, whereas it appeared in unit 1 after 168 days, but at a much lower level. The geoA gene was detected in both units, 28 days prior to the detection of geosmin in fish flesh. In addition, we detected sequences associated with Sorangium and Nannocystis (Myxococcales): members of these genera are known to produce geosmin. These sequences were observed at an earlier time in unit 2 and at a higher level than in unit 1. This study confirms the advantages of new molecular methods to understand the occurrence of geosmin production in RAS. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Probing Prokaryotic Social Behaviors with Bacterial “Lobster Traps”

PubMed Central

Connell, Jodi L.; Wessel, Aimee K.; Parsek, Matthew R.; Ellington, Andrew D.; Whiteley, Marvin; Shear, Jason B.

2010-01-01

Bacteria are social organisms that display distinct behaviors/phenotypes when present in groups. These behaviors include the abilities to construct antibiotic-resistant sessile biofilm communities and to communicate with small signaling molecules (quorum sensing [QS]). Our understanding of biofilms and QS arises primarily from in vitro studies of bacterial communities containing large numbers of cells, often greater than 108 bacteria; however, in nature, bacteria often reside in dense clusters (aggregates) consisting of significantly fewer cells. Indeed, bacterial clusters containing 101 to 105 cells are important for transmission of many bacterial pathogens. Here, we describe a versatile strategy for conducting mechanistic studies to interrogate the molecular processes controlling antibiotic resistance and QS-mediated virulence factor production in high-density bacterial clusters. This strategy involves enclosing a single bacterium within three-dimensional picoliter-scale microcavities (referred to as bacterial “lobster traps”) defined by walls that are permeable to nutrients, waste products, and other bioactive small molecules. Within these traps, bacteria divide normally into extremely dense (1012 cells/ml) clonal populations with final population sizes similar to that observed in naturally occurring bacterial clusters. Using these traps, we provide strong evidence that within low-cell-number/high-density bacterial clusters, QS is modulated not only by bacterial density but also by population size and flow rate of the surrounding medium. We also demonstrate that antibiotic resistance develops as cell density increases, with as few as ~150 confined bacteria exhibiting an antibiotic-resistant phenotype similar to biofilm bacteria. Together, these findings provide key insights into clinically relevant phenotypes in low-cell-number/high-density bacterial populations. PMID:21060734

Rydberg aggregates

NASA Astrophysics Data System (ADS)

Wüster, S.; Rost, J.-M.

2018-02-01

We review Rydberg aggregates, assemblies of a few Rydberg atoms exhibiting energy transport through collective eigenstates, considering isolated atoms or assemblies embedded within clouds of cold ground-state atoms. We classify Rydberg aggregates, and provide an overview of their possible applications as quantum simulators for phenomena from chemical or biological physics. Our main focus is on flexible Rydberg aggregates, in which atomic motion is an essential feature. In these, simultaneous control over Rydberg-Rydberg interactions, external trapping and electronic energies, allows Born-Oppenheimer surfaces for the motion of the entire aggregate to be tailored as desired. This is illustrated with theory proposals towards the demonstration of joint motion and excitation transport, conical intersections and non-adiabatic effects. Additional flexibility for quantum simulations is enabled by the use of dressed dipole-dipole interactions or the embedding of the aggregate in a cold gas or Bose-Einstein condensate environment. Finally we provide some guidance regarding the parameter regimes that are most suitable for the realization of either static or flexible Rydberg aggregates based on Li or Rb atoms. The current status of experimental progress towards enabling Rydberg aggregates is also reviewed.

Propionibacterium-Produced Coproporphyrin III Induces Staphylococcus aureus Aggregation and Biofilm Formation

PubMed Central

Wollenberg, Michael S.; Claesen, Jan; Escapa, Isabel F.; Aldridge, Kelly L.; Fischbach, Michael A.

2014-01-01

ABSTRACT The majority of bacteria detected in the nostril microbiota of most healthy adults belong to three genera: Propionibacterium, Corynebacterium, and Staphylococcus. Among these staphylococci is the medically important bacterium Staphylococcus aureus. Almost nothing is known about interspecies interactions among bacteria in the nostrils. We observed that crude extracts of cell-free conditioned medium from Propionibacterium spp. induce S. aureus aggregation in culture. Bioassay-guided fractionation implicated coproporphyrin III (CIII), the most abundant extracellular porphyrin produced by human-associated Propionibacterium spp., as a cause of S. aureus aggregation. This aggregation response depended on the CIII dose and occurred during early stationary-phase growth, and a low pH (~4 to 6) was necessary but was not sufficient for its induction. Additionally, CIII induced plasma-independent S. aureus biofilm development on an abiotic surface in multiple S. aureus strains. In strain UAMS-1, CIII stimulation of biofilm depended on sarA, a key biofilm regulator. This study is one of the first demonstrations of a small-molecule-mediated interaction among medically relevant members of the nostril microbiota and the first description of a role for CIII in bacterial interspecies interactions. Our results indicate that CIII may be an important mediator of S. aureus aggregation and/or biofilm formation in the nostril or other sites inhabited by Propionibacterium spp. and S. aureus. PMID:25053784

ATPase domain and interdomain linker play a key role in aggregation of mitochondrial Hsp70 chaperone Ssc1.

PubMed

Blamowska, Marta; Sichting, Martin; Mapa, Koyeli; Mokranjac, Dejana; Neupert, Walter; Hell, Kai

2010-02-12

The co-chaperone Hep1 is required to prevent the aggregation of mitochondrial Hsp70 proteins. We have analyzed the interaction of Hep1 with mitochondrial Hsp70 (Ssc1) and the determinants in Ssc1 that make it prone to aggregation. The ATPase and peptide binding domain (PBD) of Hsp70 proteins are connected by a linker segment that mediates interdomain communication between the domains. We show here that the minimal Hep1 binding entity of Ssc1 consists of the ATPase domain and the interdomain linker. In the absence of Hep1, the ATPase domain with the interdomain linker had the tendency to aggregate, in contrast to the ATPase domain with the mutated linker segment or without linker, and in contrast to the PBD. The closest homolog of Ssc1, bacterial DnaK, and a Ssc1 chimera, in which a segment of the ATPase domain of Ssc1 was replaced by the corresponding segment from DnaK, did not aggregate in Delta hep1 mitochondria. The propensity to aggregate appears to be a specific property of the mitochondrial Hsp70 proteins. The ATPase domain in combination with the interdomain linker is crucial for aggregation of Ssc1. In conclusion, our results suggest that interdomain communication makes Ssc1 prone to aggregation. Hep1 counteracts aggregation by binding to this aggregation-prone conformer.

ATPase Domain and Interdomain Linker Play a Key Role in Aggregation of Mitochondrial Hsp70 Chaperone Ssc1*

PubMed Central

Blamowska, Marta; Sichting, Martin; Mapa, Koyeli; Mokranjac, Dejana; Neupert, Walter; Hell, Kai

2010-01-01

The co-chaperone Hep1 is required to prevent the aggregation of mitochondrial Hsp70 proteins. We have analyzed the interaction of Hep1 with mitochondrial Hsp70 (Ssc1) and the determinants in Ssc1 that make it prone to aggregation. The ATPase and peptide binding domain (PBD) of Hsp70 proteins are connected by a linker segment that mediates interdomain communication between the domains. We show here that the minimal Hep1 binding entity of Ssc1 consists of the ATPase domain and the interdomain linker. In the absence of Hep1, the ATPase domain with the interdomain linker had the tendency to aggregate, in contrast to the ATPase domain with the mutated linker segment or without linker, and in contrast to the PBD. The closest homolog of Ssc1, bacterial DnaK, and a Ssc1 chimera, in which a segment of the ATPase domain of Ssc1 was replaced by the corresponding segment from DnaK, did not aggregate in Δhep1 mitochondria. The propensity to aggregate appears to be a specific property of the mitochondrial Hsp70 proteins. The ATPase domain in combination with the interdomain linker is crucial for aggregation of Ssc1. In conclusion, our results suggest that interdomain communication makes Ssc1 prone to aggregation. Hep1 counteracts aggregation by binding to this aggregation-prone conformer. PMID:20007714

Pattern Formation of Bacterial Colonies by Escherichia coli

NASA Astrophysics Data System (ADS)

Tokita, Rie; Katoh, Takaki; Maeda, Yusuke; Wakita, Jun-ichi; Sano, Masaki; Matsuyama, Tohey; Matsushita, Mitsugu

2009-07-01

We have studied the morphological diversity and change in bacterial colonies, using the bacterial species Escherichia coli, as a function of both agar concentration Ca and nutrient concentration Cn. We observed various colony patterns, classified them into four types by pattern characteristics and established a morphological diagram by dividing it into four regions. They are regions A [diffusion-limited aggregation (DLA)-like], B (Eden-like), C (concentric-ring), and D (fluid-spreading). In particular, we have observed a concentric-ring colony growth for E. coli. We focused on the periodic growth in region C and obtained the following results: (i) A colony grows cyclically with the growing front repeating an advance (migration phase) and a momentary rest (consolidation phase) alternately. (ii) The growth width L and the bulge width W in one cycle decrease asymptotically to certain values, when Ca is increased. (iii) L does not depend on Cn, while W is an increasing function of Cn. Plausible mechanisms are proposed to explain the experimental results, by comparing them with those obtained for other bacterial species such as Proteus mirabilis and Bacillus subtilis.

Concepts and tools to exploit the potential of bacterial inclusion bodies in protein science and biotechnology.

PubMed

Gatti-Lafranconi, Pietro; Natalello, Antonino; Ami, Diletta; Doglia, Silvia Maria; Lotti, Marina

2011-07-01

Cells have evolved complex and overlapping mechanisms to protect their proteins from aggregation. However, several reasons can cause the failure of such defences, among them mutations, stress conditions and high rates of protein synthesis, all common consequences of heterologous protein production. As a result, in the bacterial cytoplasm several recombinant proteins aggregate as insoluble inclusion bodies. The recent discovery that aggregated proteins can retain native-like conformation and biological activity has opened the way for a dramatic change in the means by which intracellular aggregation is approached and exploited. This paper summarizes recent studies towards the direct use of inclusion bodies in biotechnology and for the detection of bottlenecks in the folding pathways of specific proteins. We also review the major biophysical methods available for revealing fine structural details of aggregated proteins and which information can be obtained through these techniques. © 2011 The Authors Journal compilation © 2011 FEBS.

Attempts to improve nitrogen utilization efficiency of aquaponics through nitrifies addition and filler gradation.

PubMed

Zou, Yina; Hu, Zhen; Zhang, Jian; Xie, Huijun; Liang, Shuang; Wang, Jinhe; Yan, Runxin

2016-04-01

Aquaponics has attracted worldwide attention in recent years and is considered as an alternative technology for conventional aquaculture. In this study, common carp (Cyprinus carpio) and pakchoi (Brassica chinensis) were cultured in lab-scale aquaponics, and attempts were conducted to enhance its nitrogen utilization efficiency (NUE) through two optimization methods, i.e., nitrifies addition (NA) and filler gradation (FG). Results showed that NA and FG could improve the NUE of aquaponics by 8.8 and 16.0%, respectively, compared with control. The total ammonia (TAN) and nitrite (NO2(-)) concentrations in NA and FG systems were maintained at relatively low level (TAN < 0.5 mg/L, NO2(-) < 0.1 mg/L), which demonstrated that both the NA and FG could provide non-toxic water environment for fish culture. Nitrous oxide conversion ratio of the control, NA, and FG were 0.8, 1.2, and 1.7%, respectively, indicating that media-based aquaponics also contributed to global warming. Although the two proposed attempts in this study caused more N2O emission, they made new breakthrough in improving the NUE of aquaponics.

SMU.940 regulates dextran-dependent aggregation and biofilm formation in Streptococcus mutans.

PubMed

Senpuku, Hidenobu; Yonezawa, Hideo; Yoneda, Saori; Suzuki, Itaru; Nagasawa, Ryo; Narisawa, Naoki

2018-02-01

The oral bacterium Streptococcus mutans is the principal agent in the development of dental caries. Biofilm formation by S. mutans requires bacterial attachment, aggregation, and glucan formation on the tooth surface under sucrose supplementation conditions. Our previous microarray analysis of clinical strains identified 74 genes in S. mutans that were related to biofilm morphology; however, the roles of almost all of these genes in biofilm formation are poorly understood. We investigated the effects of 21 genes randomly selected from our previous study regarding S. mutans biofilm formation, regulation by the complement pathway, and responses to competence-stimulating peptide. Eight competence-stimulating peptide-dependent genes were identified, and their roles in biofilm formation and aggregation were examined by mutational analyses of the S. mutansUA159 strain. Of these eight genes, the inactivation of the putative hemolysin III family SMU.940 gene of S. mutansUA159 promoted rapid dextran-dependent aggregation and biofilm formation in tryptic soy broth without dextrose (TSB) with 0.25% glucose and slightly reduced biofilm formation in TSB with 0.25% sucrose. The SMU.940 mutant showed higher expression of GbpC and gbpC gene than wild-type. GbpC is known to be involved in the dextran-dependent aggregation of S. mutans. An SMU.940-gbpC double mutant strain was constructed in the SMU.940 mutant background. The gbpC mutation completely abolished the dextran-dependent aggregation of the SMU.940 mutant. In addition, the aggregation of the mutant was abrogated by dextranase. These findings suggest that SMU.940 controls GbpC expression, and contributes to the regulation of dextran-dependent aggregation and biofilm formation. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Biological deammonification of livestock effluents after anaerobic digestion using specialized bacterial cultures

USDA-ARS?s Scientific Manuscript database

We investigated a deammonification process for the removal of ammonia from anaerobi digestion (AD) effluents. This process is autotrophic and removes N without carbon. Instant deammonification reaction was obtained by mixing a high performance nitrifying sludge (HPNS) (NRRL B-50298) with anammox slu...

Surface characteristics of spacecraft components affect the aggregation of microorganisms and may lead to different survival rates of bacteria on Mars landers.

PubMed

Schuerger, Andrew C; Richards, Jeffrey T; Hintze, Paul E; Kern, Roger G

2005-08-01

Layers of dormant endospores of Bacillus subtilis HA101 were applied to eight different spacecraft materials and exposed to martian conditions of low pressure (8.5 mbar), low temperature (-10 degrees C), and high CO(2) gas composition and irradiated with a Mars-normal ultraviolet (UV-visible- near-infrared spectrum. Bacterial layers were exposed to either 1 min or 1 h of Mars-normal UV irradiation, which simulated clear-sky conditions on equatorial Mars (0.1 tau). When exposed to 1 min of Mars UV irradiation, the numbers of viable endospores of B. subtilis were reduced three to four orders of magnitude for two brands of aluminum (Al), stainless steel, chemfilm-treated Al, clear-anodized Al, and black-anodized Al coupons. In contrast, bacterial survival was reduced only one to two orders of magnitude for endospores on the non-metal materials astroquartz and graphite composite when bacterial endospores were exposed to 1 min of Mars UV irradiation. When bacterial monolayers were exposed to 1 h of Mars UV irradiation, no viable bacteria were recovered from the six metal coupons listed above. In contrast, bacterial survival was reduced only two to three orders of magnitude for spore layers on astroquartz and graphite composite exposed to 1 h of Mars UV irradiation. Scanning electron microscopy images of the bacterial monolayers on all eight spacecraft materials revealed that endospores of B. subtilis formed large aggregates of multilayered spores on astroquartz and graphite composite, but not on the other six spacecraft materials. It is likely that the formation of multilayered aggregates of endospores on astroquartz and graphite composite is responsible for the enhanced survival of bacterial cells on these materials.

Surface characteristics of spacecraft components affect the aggregation of microorganisms and may lead to different survival rates of bacteria on Mars landers

NASA Technical Reports Server (NTRS)

Schuerger, Andrew C.; Richards, Jeffrey T.; Hintze, Paul E.; Kern, Roger G.

2005-01-01

Layers of dormant endospores of Bacillus subtilis HA101 were applied to eight different spacecraft materials and exposed to martian conditions of low pressure (8.5 mbar), low temperature (-10 degrees C), and high CO(2) gas composition and irradiated with a Mars-normal ultraviolet (UV-visible- near-infrared spectrum. Bacterial layers were exposed to either 1 min or 1 h of Mars-normal UV irradiation, which simulated clear-sky conditions on equatorial Mars (0.1 tau). When exposed to 1 min of Mars UV irradiation, the numbers of viable endospores of B. subtilis were reduced three to four orders of magnitude for two brands of aluminum (Al), stainless steel, chemfilm-treated Al, clear-anodized Al, and black-anodized Al coupons. In contrast, bacterial survival was reduced only one to two orders of magnitude for endospores on the non-metal materials astroquartz and graphite composite when bacterial endospores were exposed to 1 min of Mars UV irradiation. When bacterial monolayers were exposed to 1 h of Mars UV irradiation, no viable bacteria were recovered from the six metal coupons listed above. In contrast, bacterial survival was reduced only two to three orders of magnitude for spore layers on astroquartz and graphite composite exposed to 1 h of Mars UV irradiation. Scanning electron microscopy images of the bacterial monolayers on all eight spacecraft materials revealed that endospores of B. subtilis formed large aggregates of multilayered spores on astroquartz and graphite composite, but not on the other six spacecraft materials. It is likely that the formation of multilayered aggregates of endospores on astroquartz and graphite composite is responsible for the enhanced survival of bacterial cells on these materials.

Licochalcones extracted from Glycyrrhiza inflata inhibit platelet aggregation accompanied by inhibition of COX-1 activity

PubMed Central

Okuda-Tanino, Asa; Sugawara, Daiki; Tashiro, Takumi; Iwashita, Masaya; Obara, Yutaro; Moriya, Takahiro; Tsushima, Chisato; Saigusa, Daisuke; Tomioka, Yoshihisa; Ishii, Kuniaki; Nakahata, Norimichi

2017-01-01

Licochalcones extracted from Glycyrrhiza inflata are known to have a variety of biological properties such as anti-inflammatory, anti-bacterial, and anti-tumor activities, but their action on platelet aggregation has not yet been reported. Therefore, in this study we investigated the effects of licochalcones on platelet aggregation. Collagen and U46619, a thromboxane A2 receptor agonist, caused rabbit platelet aggregation, which was reversed by pretreatment with licochalcones A, C and D in concentration-dependent manners. Among these compounds, licochalcone A caused the most potent inhibitory effect on collagen-induced platelet aggregation. However, the licochalcones showed marginal inhibitory effects on thrombin or ADP-induced platelet aggregation. In addition to rabbit platelets, licochalcone A attenuated collagen-induced aggregation in human platelets. Because licochalcone A also inhibited arachidonic acid-induced platelet aggregation and production of thromboxane A2 induced by collagen in intact platelets, we further examined the direct interaction of licochalcone A with cyclooxygenase (COX)-1. As expected, licochalcone A caused an inhibitory effect on both COX-1 and COX-2 in vitro. Regarding the effect of licochalcone A on COX-1 enzyme reaction kinetics, although licochalcone A showed a stronger inhibition of prostaglandin E2 synthesis induced by lower concentrations of arachidonic acid, Vmax values in the presence or absence of licochalcone A were comparable, suggesting that it competes with arachidonic acid at the same binding site on COX-1. These results suggest that licochalcones inhibit collagen-induced platelet aggregation accompanied by inhibition of COX-1 activity. PMID:28282426

Relative distance between tracers as a measure of diffusivity within moving aggregates

NASA Astrophysics Data System (ADS)

Pönisch, Wolfram; Zaburdaev, Vasily

2018-02-01

Tracking of particles, be it a passive tracer or an actively moving bacterium in the growing bacterial colony, is a powerful technique to probe the physical properties of the environment of the particles. One of the most common measures of particle motion driven by fluctuations and random forces is its diffusivity, which is routinely obtained by measuring the mean squared displacement of the particles. However, often the tracer particles may be moving in a domain or an aggregate which itself experiences some regular or random motion and thus masks the diffusivity of tracers. Here we provide a method for assessing the diffusivity of tracer particles within mobile aggregates by measuring the so-called mean squared relative distance (MSRD) between two tracers. We provide analytical expressions for both the ensemble and time averaged MSRD allowing for direct identification of diffusivities from experimental data.

Pathological-Condition-Driven Construction of Supramolecular Nanoassemblies for Bacterial Infection Detection.

PubMed

Li, Li-Li; Ma, Huai-Lei; Qi, Guo-Bin; Zhang, Di; Yu, Faquan; Hu, Zhiyuan; Wang, Hao

2016-01-13

A pyropheophorbide-α-based building block (Ppa-PLGVRG-Van) can be used to construct self-aggregated superstructures in vivo for highly specific and sensitive diagnosis of bacterial infection by noninvasive photoacoustic tomography. This in vivo supramolecular chemistry approach opens a new avenue for efficient, rapid, and early-stage disease diagnosis with high sensitivity and specificity. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A mathematical approach to molecular organization and proteolytic disintegration of bacterial inclusion bodies.

PubMed

Cubarsi, R; Carrió, M M; Villaverde, A

2005-09-01

The in vivo proteolytic digestion of bacterial inclusion bodies (IBs) and the kinetic analysis of the resulting protein fragments is an interesting approach to investigate the molecular organization of these unconventional protein aggregates. In this work, we describe a set of mathematical instruments useful for such analysis and interpretation of observed data. These methods combine numerical estimation of digestion rate and approximation of its high-order derivatives, modelling of fragmentation events from a mixture of Poisson processes associated with differentiated protein species, differential equations techniques in order to estimate the mixture parameters, an iterative predictor-corrector algorithm for describing the flow diagram along the cascade process, as well as least squares procedures with minimum variance estimates. The models are formulated and compared with data, and successively refined to better match experimental observations. By applying such procedures as well as newer improved algorithms of formerly developed equations, it has been possible to model, for two kinds of bacterially produced aggregation prone recombinant proteins, their cascade digestion process that has revealed intriguing features of the IB-forming polypeptides.

[Study of shear rate in modified airlift nitrifying bioreactor].

PubMed

Jin, Ren-cun; Zheng, Ping

2006-06-01

The characteristics of shear rate in an airlift nitrifying bioreactor and its influencing factors were studied. The results showed that the shear rate was different in different sections of the bioreactor. With inlet gas flowrate at 430 approximately 2700 L x h(-1), the overall shear rate was (0.702 approximately 3.13) x 10(5) s(-1), shear rate in riser was (1.07 approximately 31.3) x 10(5) s(-1) and in gas-liquid separator was (1.12 approximately 25.0) x 10(5) s(-1), respectively. It indicates that the highest shear rates prevailed in the riser part of bioreactor. The operational variables and the bioreactor configurations exerted a significant influence on the shear level of the bioreactor. When inlet gas flowrate was raised from 1300 to 2700 L x h(-1), shear rate in riser and separator ascended first and then descended subsequently. The diameter of draft tube (d) was negatively correlated with shear rate. When the draft tube with diameter of 5.5 cm was installed, the shear rates in riser, separator and overall shear rate were 85.5%, 82.3% and 80.6%, respectively less as compared with that with diameter of 4.0 cm. The number of static mixers (N) was positively correlated with the shear rate. When d was set at 4.0 cm, with N of 10 and 39, the shear rates in riser were 6.14 and 7.97 times higher respectively, than that of conventional bioreactor. The ratio of maximum local shear rate to overall shear rate was 3.68 approximately 7.66, and the homogeneity of the shear field in airlift bioreactors could be improved if d and N were set at 5.5 cm and 10 approximately 13, respectively.

Azaphilones inhibit tau aggregation and dissolve tau aggregates in vitro.

PubMed

Paranjape, Smita R; Riley, Andrew P; Somoza, Amber D; Oakley, C Elizabeth; Wang, Clay C C; Prisinzano, Thomas E; Oakley, Berl R; Gamblin, T Chris

2015-05-20

The aggregation of the microtubule-associated protein tau is a seminal event in many neurodegenerative diseases, including Alzheimer's disease. The inhibition or reversal of tau aggregation is therefore a potential therapeutic strategy for these diseases. Fungal natural products have proven to be a rich source of useful compounds having wide varieties of biological activities. We have previously screened Aspergillus nidulans secondary metabolites for their ability to inhibit tau aggregation in vitro using an arachidonic acid polymerization protocol. One aggregation inhibitor identified was asperbenzaldehyde, an intermediate in azaphilone biosynthesis. We therefore tested 11 azaphilone derivatives to determine their tau assembly inhibition properties in vitro. All compounds tested inhibited tau filament assembly to some extent, and four of the 11 compounds had the advantageous property of disassembling preformed tau aggregates in a dose-dependent fashion. The addition of these compounds to the tau aggregates reduced both the total length and number of tau polymers. The most potent compounds were tested in in vitro reactions to determine whether they interfere with tau's normal function of stabilizing microtubules (MTs). We found that they did not completely inhibit MT assembly in the presence of tau. These derivatives are very promising lead compounds for tau aggregation inhibitors and, more excitingly, for compounds that can disassemble pre-existing tau filaments. They also represent a new class of anti-tau aggregation compounds with a novel structural scaffold.

A Combination of Biochar–Mineral Complexes and Compost Improves Soil Bacterial Processes, Soil Quality, and Plant Properties

PubMed Central

Ye, Jun; Zhang, Rui; Nielsen, Shaun; Joseph, Stephen D.; Huang, Danfeng; Thomas, Torsten

2016-01-01

Organic farming avoids the use of synthetic fertilizers and promises food production with minimal environmental impact, however this farming practice does not often result in the same productivity as conventional farming. In recent years, biochar has received increasing attention as an agricultural amendment and by coating it with minerals to form biochar–mineral complex (BMC) carbon retention and nutrient availability can be improved. However, little is known about the potential of BMC in improving organic farming. We therefore investigated here how soil, bacterial and plant properties respond to a combined treatment of BMC and an organic fertilizer, i.e., a compost based on poultry manure. In a pakchoi pot trial, BMC and compost showed synergistic effects on soil properties, and specifically by increasing nitrate content. Soil nitrate has been previously observed to increase leaf size and we correspondingly saw an increase in the surface area of pakchoi leaves under the combined treatment of BMC and composted chicken manure. The increase in soil nitrate was also correlated with an enrichment of bacterial nitrifiers due to BMC. Additionally, we observed that the bacteria present in the compost treatment had a high turnover, which likely facilitated organic matter degradation and a reduction of potential pathogens derived from the manure. Overall our results demonstrate that a combination of BMC and compost can stimulate microbial process in organic farming that result in better vegetable production and improved soil properties for sustainable farming. PMID:27092104

A Combination of Biochar-Mineral Complexes and Compost Improves Soil Bacterial Processes, Soil Quality, and Plant Properties.

PubMed

Ye, Jun; Zhang, Rui; Nielsen, Shaun; Joseph, Stephen D; Huang, Danfeng; Thomas, Torsten

2016-01-01

Organic farming avoids the use of synthetic fertilizers and promises food production with minimal environmental impact, however this farming practice does not often result in the same productivity as conventional farming. In recent years, biochar has received increasing attention as an agricultural amendment and by coating it with minerals to form biochar-mineral complex (BMC) carbon retention and nutrient availability can be improved. However, little is known about the potential of BMC in improving organic farming. We therefore investigated here how soil, bacterial and plant properties respond to a combined treatment of BMC and an organic fertilizer, i.e., a compost based on poultry manure. In a pakchoi pot trial, BMC and compost showed synergistic effects on soil properties, and specifically by increasing nitrate content. Soil nitrate has been previously observed to increase leaf size and we correspondingly saw an increase in the surface area of pakchoi leaves under the combined treatment of BMC and composted chicken manure. The increase in soil nitrate was also correlated with an enrichment of bacterial nitrifiers due to BMC. Additionally, we observed that the bacteria present in the compost treatment had a high turnover, which likely facilitated organic matter degradation and a reduction of potential pathogens derived from the manure. Overall our results demonstrate that a combination of BMC and compost can stimulate microbial process in organic farming that result in better vegetable production and improved soil properties for sustainable farming.

Microbial characterization of nitrification in a shallow, nitrogen-contaminated aquifer, Cape Cod, Massachusetts and detection of a novel cluster associated with nitrifying Betaproteobacteria

USGS Publications Warehouse

Miller, D.N.; Smith, R.L.

2009-01-01

Groundwater nitrification is a poorly characterized process affecting the speciation and transport of nitrogen. Cores from two sites in a plume of contamination were examined using culture-based and molecular techniques targeting nitrification processes. The first site, located beneath a sewage effluent infiltration bed, received treated effluent containing O2 (> 300????M) and NH4+ (51-800????M). The second site was 2.5??km down-gradient near the leading edge of the ammonium zone within the contaminant plume and featured vertical gradients of O2, NH4+, and NO3- (0-300, 0-500, and 100-200????M with depth, respectively). Ammonia- and nitrite-oxidizers enumerated by the culture-based MPN method were low in abundance at both sites (1.8 to 350??g- 1 and 33 to 35,000??g- 1, respectively). Potential nitrifying activity measured in core material in the laboratory was also very low, requiring several weeks for products to accumulate. Molecular analysis of aquifer DNA (nested PCR followed by cloning and 16S rDNA sequencing) detected primarily sequences associated with the Nitrosospira genus throughout the cores at the down-gradient site and a smaller proportion from the Nitrosomonas genus in the deeper anoxic, NH4+ zone at the down-gradient site. Only a single Nitrosospira sequence was detected beneath the infiltration bed. Furthermore, the majority of Nitrosospira-associated sequences represent an unrecognized cluster. We conclude that an uncharacterized group associated with Nitrosospira dominate at the geochemically stable, down-gradient site, but found little evidence for Betaproteobacteria nitrifiers beneath the infiltration beds where geochemical conditions were more variable.

α- and β-Proteobacteria Control the Consumption and Release of Amino Acids on Lake Snow Aggregates

PubMed Central

Schweitzer, Bernhard; Huber, Ingrid; Amann, Rudolf; Ludwig, Wolfgang; Simon, Meinhard

2001-01-01

We analyzed the composition of aggregate (lake snow)-associated bacterial communities in Lake Constance from 1994 until 1996 between a depth of 25 m and the sediment surface at 110 m by fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes of various specificity. In addition, we experimentally examined the turnover of dissolved amino acids and carbohydrates together with the microbial colonization of aggregates formed in rolling tanks in the lab. Generally, between 40 and more than 80% of the microbes enumerated by DAPI staining (4′,6′-diamidino-2-phenylindole) were detected as Bacteria by the probe EUB338. At a depth of 25 m, 10.5% ± 7.9% and 14.2% ± 10.2% of the DAPI cell counts were detected by probes specific for α- and β-Proteobacteria. These proportions increased to 12.0% ± 3.3% and 54.0% ± 5.9% at a depth of 50 m but decreased again at the sediment surface at 110 m to 2.7% ± 1.4% and 41.1% ± 8.4%, indicating a clear dominance of β-Proteobacteria at depths of 50 and 110 m, where aggregates have an age of 3 to 5 and 8 to 11 days, respectively. From 50 m to the sediment surface, cells detected by a Cytophaga/Flavobacteria-specific probe (CF319a) comprised increasing proportions up to 18% of the DAPI cell counts. γ-Proteobacteria always comprised minor proportions of the aggregate-associated bacterial community. Using only two probes highly specific for clusters of bacteria closely related to Sphingomonas species and Brevundimonas diminuta, we identified between 16 and 60% of the α-Proteobacteria. In addition, with three probes highly specific for close relatives of the β-Proteobacteria Duganella zoogloeoides (formerly Zoogloea ramigera), Acidovorax facilis, and Hydrogenophaga palleroni, bacteria common in activated sludge, 42 to 70% of the β-Proteobacteria were identified. In the early phase (<20 h) of 11 of the 15 experimental incubations of aggregates, dissolved amino acids were consumed by the aggregate

Differentiating sepsis from non-infectious systemic inflammation based on microvesicle-bacteria aggregation

NASA Astrophysics Data System (ADS)

Herrmann, I. K.; Bertazzo, S.; O'Callaghan, D. J. P.; Schlegel, A. A.; Kallepitis, C.; Antcliffe, D. B.; Gordon, A. C.; Stevens, M. M.

2015-08-01

Sepsis is a severe medical condition and a leading cause of hospital mortality. Prompt diagnosis and early treatment has a significant, positive impact on patient outcome. However, sepsis is not always easy to diagnose, especially in critically ill patients. Here, we present a conceptionally new approach for the rapid diagnostic differentiation of sepsis from non-septic intensive care unit patients. Using advanced microscopy and spectroscopy techniques, we measure infection-specific changes in the activity of nano-sized cell-derived microvesicles to bind bacteria. We report on the use of a point-of-care-compatible microfluidic chip to measure microvesicle-bacteria aggregation and demonstrate rapid (<=1.5 hour) and reliable diagnostic differentiation of bacterial infection from non-infectious inflammation in a double-blind pilot study. Our study demonstrates the potential of microvesicle activities for sepsis diagnosis and introduces microvesicle-bacteria aggregation as a potentially useful parameter for making early clinical management decisions.Sepsis is a severe medical condition and a leading cause of hospital mortality. Prompt diagnosis and early treatment has a significant, positive impact on patient outcome. However, sepsis is not always easy to diagnose, especially in critically ill patients. Here, we present a conceptionally new approach for the rapid diagnostic differentiation of sepsis from non-septic intensive care unit patients. Using advanced microscopy and spectroscopy techniques, we measure infection-specific changes in the activity of nano-sized cell-derived microvesicles to bind bacteria. We report on the use of a point-of-care-compatible microfluidic chip to measure microvesicle-bacteria aggregation and demonstrate rapid (<=1.5 hour) and reliable diagnostic differentiation of bacterial infection from non-infectious inflammation in a double-blind pilot study. Our study demonstrates the potential of microvesicle activities for sepsis diagnosis and

Direct Conversion of an Enzyme from Native-like to Amyloid-like Aggregates within Inclusion Bodies.

PubMed

Elia, Francesco; Cantini, Francesca; Chiti, Fabrizio; Dobson, Christopher Martin; Bemporad, Francesco

2017-06-20

The acylphosphatase from Sulfolobus solfataricus (Sso AcP) is a globular protein able to aggregate in vitro from a native-like conformational ensemble without the need for a transition across the major unfolding energy barrier. This process leads to the formation of assemblies in which the protein retains its native-like structure, which subsequently convert into amyloid-like aggregates. Here, we investigate the mechanism by which Sso AcP aggregates in vivo to form bacterial inclusion bodies after expression in E. coli. Shortly after the initiation of expression, Sso AcP is incorporated into inclusion bodies as a native-like protein, still exhibiting small but significant enzymatic activity. Additional experiments revealed that this overall process of aggregation is enhanced by the presence of the unfolded N-terminal region of the sequence and by destabilization of the globular segment of the protein. At later times, the Sso AcP molecules in the inclusion bodies lose their native-like properties and convert into β-sheet-rich amyloid-like structures, as indicated by their ability to bind thioflavin T and Congo red. These results show that the aggregation behavior of this protein is similar in vivo to that observed in vitro, and that, at least for a predominant part of the protein population, the transition from a native to an amyloid-like structure occurs within the aggregate state. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Effects of Grape Xylem Sap and Cell-Wall Constituents on In Vitro Growth, Biofilm Formation and Cellular Aggregation of Xylella fastidiosa

USDA-ARS?s Scientific Manuscript database

Purified cell-wall constituents or grape xylem sap added to media affected in vitro growth, biofilm formation, cell aggregation and gene expression of Xylella fastidiosa. Media containing xylem sap from Pierce’s disease (PD)-susceptible plants provided better support for bacterial growth and biofil...

Marine Synechococcus Aggregation

NASA Astrophysics Data System (ADS)

Neuer, S.; Deng, W.; Cruz, B. N.; Monks, L.

2016-02-01

Cyanobacteria are considered to play an important role in the oceanic biological carbon pump, especially in oligotrophic regions. But as single cells are too small to sink, their carbon export has to be mediated by aggregate formation and possible consumption by zooplankton producing sinking fecal pellets. Here we report results on the aggregation of the ubiquitous marine pico-cyanobacterium Synechococcus as a model organism. We first investigated the mechanism behind such aggregation by studying the potential role of transparent exopolymeric particles (TEP) and the effects of nutrient (nitrogen or phosphorus) limitation on the TEP production and aggregate formation of these pico-cyanobacteria. We further studied the aggregation and subsequent settling in roller tanks and investigated the effects of the clays kaolinite and bentonite in a series of concentrations. Our results show that despite of the lowered growth rates, Synechococcus in nutrient limited cultures had larger cell-normalized TEP production, formed a greater volume of aggregates, and resulted in higher settling velocities compared to results from replete cultures. In addition, we found that despite their small size and lack of natural ballasting minerals, Synechococcus cells could still form aggregates and sink at measureable velocities in seawater. Clay minerals increased the number and reduced the size of aggregates, and their ballasting effects increased the sinking velocity and carbon export potential of aggregates. In comparison with the Synechococcus, we will also present results of the aggregation of the pico-cyanobacterium Prochlorococcus in roller tanks. These results contribute to our understanding in the physiology of marine Synechococcus as well as their role in the ecology and biogeochemistry in oligotrophic oceans.

Changes in carbon stability and microbial activity in size fractions of micro-aggregates in a rice soil chronosequence under long term rice cultivation

NASA Astrophysics Data System (ADS)

Pan, Genxing; Liu, Yalong; Wang, Ping; Li, Lianqinfg; Cheng, Kun; Zheng, Jufeng; Zhang, Xuhui; Zheng, Jinwei; Bian, Rongjun; Ding, Yuanjun; Ma, Chong

2016-04-01

Recent studies have shown soil carbon sequestration through physical protection of relative labile carbon intra micro-aggregates with formation of large sized macro-aggregates under good management of soil and agricultural systems. While carbon stabilization had been increasingly concerned as ecosystem properties, the mechanisms underspin bioactivity of soil carbon with increased carbon stability has been still poorly understood. In this study, topsoil samples were collected from rice soils derived from salt marsh under different length of rice cultivation up to 700 years from eastern China. Particle size fractions (PSF) of soil aggregates were separated using a low energy dispersion protocol. Carbon fractions in the PSFs were analyzed either with FTIR spectroscopy. Soil microbial community of bacterial, fungal and archaeal were analyzed with molecular fingerprinting using specific gene primers. Soil respiration and carbon gain from amended maize as well as enzyme activities were measured using lab incubation protocols. While the PSFs were dominated by the fine sand (200-20μm) and silt fraction (20-2μm), the mass proportion both of sand (2000-200μm) and clay (<2μm) fraction increased with prolonged rice cultivation, giving rise to an increasing trend of mean weight diameter of soil aggregates (also referred to aggregate stability). Soil organic carbon was found most enriched in coarse sand fraction (40-60g/kg), followed by the clay fraction (20-24.5g/kg), but depleted in the silt fraction (~10g/kg). Phenolic and aromatic carbon as recalcitrant pool were high (33-40% of total SOC) in both coarse sand and clay fractions than in both fine sand and silt fractions (20-29% of total SOC). However, the ratio of LOC/total SOC showed a weak decreasing trend with decreasing size of the aggregate fractions. Total gene content in the size fractions followed a similar trend to that of SOC. Bacterial and archaeal gene abundance was concentrated in both sand and clay fractions

Measuring and modeling the oxygen profile in a nitrifying Moving Bed Biofilm Reactor.

PubMed

Masić, Alma; Bengtsson, Jessica; Christensson, Magnus

2010-09-01

In this paper we determine the oxygen profile in a biofilm on suspended carriers in two ways: firstly by microelectrode measurements and secondly by a simple mathematical model. The Moving Bed Biofilm Reactor is well-established for wastewater treatment where bacteria grow as a biofilm on the protective surfaces of suspended carriers. The flat shaped BiofilmChip P was developed to allow good conditions for transport of substrates into the biofilm. The oxygen profile was measured in situ the nitrifying biofilm with a microelectrode and it was simulated with a one-dimensional mathematical model. We extended the model by adding a CSTR equation, to connect the reactor to the biofilm through the boundary conditions. We showed the dependence of the thickness of the mass transfer boundary layer on the bulk flow rate. Finally, we estimated the erosion parameter lambda to increase the concordance between the measured and simulated profiles. This lead to a simple empirical relationship between lambda and the flow rate. The data gathered by in situ microelectrode measurements can, together with the mathematical model, be used in predictive modeling and give more insight in the design of new carriers, with the ambition of making process operation more energy efficient. Copyright 2010 Elsevier Inc. All rights reserved.

Isolation of high-salinity-tolerant bacterial strains, Enterobacter sp., Serratia sp., Yersinia sp., for nitrification and aerobic denitrification under cyanogenic conditions.

PubMed

Mpongwana, N; Ntwampe, S K O; Mekuto, L; Akinpelu, E A; Dyantyi, S; Mpentshu, Y

2016-01-01

Cyanides (CN(-)) and soluble salts could potentially inhibit biological processes in wastewater treatment plants (WWTPs), such as nitrification and denitrification. Cyanide in wastewater can alter metabolic functions of microbial populations in WWTPs, thus significantly inhibiting nitrifier and denitrifier metabolic processes, rendering the water treatment processes ineffective. In this study, bacterial isolates that are tolerant to high salinity conditions, which are capable of nitrification and aerobic denitrification under cyanogenic conditions, were isolated from a poultry slaughterhouse effluent. Three of the bacterial isolates were found to be able to oxidise NH(4)-N in the presence of 65.91 mg/L of free cyanide (CN(-)) under saline conditions, i.e. 4.5% (w/v) NaCl. The isolates I, H and G, were identified as Enterobacter sp., Yersinia sp. and Serratia sp., respectively. Results showed that 81% (I), 71% (G) and 75% (H) of 400 mg/L NH(4)-N was biodegraded (nitrification) within 72 h, with the rates of biodegradation being suitably described by first order reactions, with rate constants being: 4.19 h(-1) (I), 4.21 h(-1) (H) and 3.79 h(-1) (G), respectively, with correlation coefficients ranging between 0.82 and 0.89. Chemical oxygen demand (COD) removal rates were 38% (I), 42% (H) and 48% (G), over a period of 168 h with COD reduction being highest at near neutral pH.

Detection of Prosthetic Hip Infection at Revision Arthroplasty by Immunofluorescence Microscopy and PCR Amplification of the Bacterial 16S rRNA Gene

PubMed Central

Tunney, Michael M.; Patrick, Sheila; Curran, Martin D.; Ramage, Gordon; Hanna, Donna; Nixon, James R.; Gorman, Sean P.; Davis, Richard I.; Anderson, Neil

1999-01-01

In this study the detection rates of bacterial infection of hip prostheses by culture and nonculture methods were compared for 120 patients with total hip revision surgery. By use of strict anaerobic bacteriological practice during the processing of samples and without enrichment, the incidence of infection by culture of material dislodged from retrieved prostheses after ultrasonication (sonicate) was 22%. Bacteria were observed by immunofluorescence microscopy in 63% of sonicate samples with a monoclonal antibody specific for Propionibacterium acnes and polyclonal antiserum specific for Staphylococcus spp. The bacteria were present either as single cells or in aggregates of up to 300 bacterial cells. These aggregates were not observed without sonication to dislodge the biofilm. Bacteria were observed in all of the culture-positive samples, and in some cases in which only one type of bacterium was identified by culture, both coccoid and coryneform bacteria were observed by immunofluorescence microscopy. Bacteria from skin-flake contamination were readily distinguishable from infecting bacteria by immunofluorescence microscopy. Examination of skin scrapings did not reveal large aggregates of bacteria but did reveal skin cells. These were not observed in the sonicates. Bacterial DNA was detected in 72% of sonicate samples by PCR amplification of a region of the bacterial 16S rRNA gene with universal primers. All of the culture-positive samples were also positive for bacterial DNA. Evidence of high-level infiltration either of neutrophils or of lymphocytes or macrophages into associated tissue was observed in 73% of patients. Our results indicate that the incidence of prosthetic joint infection is grossly underestimated by current culture detection methods. It is therefore imperative that current clinical practice with regard to the detection and subsequent treatment of prosthetic joint infection be reassessed in the light of these results. PMID:10488193

Symbiotic Cell Differentiation and Cooperative Growth in Multicellular Aggregates

PubMed Central

Yamagishi, Jumpei F; Saito, Nen; Kaneko, Kunihiko

2016-01-01

As cells grow and divide under a given environment, they become crowded and resources are limited, as seen in bacterial biofilms and multicellular aggregates. These cells often show strong interactions through exchanging chemicals, as evident in quorum sensing, to achieve mutualism and division of labor. Here, to achieve stable division of labor, three characteristics are required. First, isogenous cells differentiate into several types. Second, this aggregate of distinct cell types shows better growth than that of isolated cells without interaction and differentiation, by achieving division of labor. Third, this cell aggregate is robust with respect to the number distribution of differentiated cell types. Indeed, theoretical studies have thus far considered how such cooperation is achieved when the ability of cell differentiation is presumed. Here, we address how cells acquire the ability of cell differentiation and division of labor simultaneously, which is also connected with the robustness of a cell society. For this purpose, we developed a dynamical-systems model of cells consisting of chemical components with intracellular catalytic reaction dynamics. The reactions convert external nutrients into internal components for cellular growth, and the divided cells interact through chemical diffusion. We found that cells sharing an identical catalytic network spontaneously differentiate via induction from cell-cell interactions, and then achieve division of labor, enabling a higher growth rate than that in the unicellular case. This symbiotic differentiation emerged for a class of reaction networks under the condition of nutrient limitation and strong cell-cell interactions. Then, robustness in the cell type distribution was achieved, while instability of collective growth could emerge even among the cooperative cells when the internal reserves of products were dominant. The present mechanism is simple and general as a natural consequence of interacting cells with

Kinetics of nitrification in a fixed biofilm reactor using dewatered sludge-fly ash composite ceramic particle as a supporting medium.

PubMed

Lee, Mong-Chuan; Lin, Yen-Hui; Yu, Huang-Wei

2014-11-01

A mathematical model system was derived to describe the kinetics of ammonium nitrification in a fixed biofilm reactor using dewatered sludge-fly ash composite ceramic particle as a supporting medium. The model incorporates diffusive mass transport and Monod kinetics. The model was solved using a combination of the orthogonal collocation method and Gear's method. A batch test was conducted to observe the nitrification of ammonium-nitrogen ([Formula: see text]-N) and the growth of nitrifying biomass. The compositions of nitrifying bacterial community in the batch kinetic test were analyzed using PCR-DGGE method. The experimental results show that the most staining intensity abundance of bands occurred on day 2.75 with the highest biomass concentration of 46.5 mg/L. Chemostat kinetic tests were performed independently to evaluate the biokinetic parameters used in the model prediction. In the column test, the removal efficiency of [Formula: see text]-N was approximately 96 % while the concentration of suspended nitrifying biomass was approximately 16 mg VSS/L and model-predicted biofilm thickness reached up to 0.21 cm in the steady state. The profiles of denaturing gradient gel electrophoresis (DGGE) of different microbial communities demonstrated that indigenous nitrifying bacteria (Nitrospira and Nitrobacter) existed and were the dominant species in the fixed biofilm process.

GEOMETRIC CROSS SECTIONS OF DUST AGGREGATES AND A COMPRESSION MODEL FOR AGGREGATE COLLISIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suyama, Toru; Wada, Koji; Tanaka, Hidekazu

2012-07-10

Geometric cross sections of dust aggregates determine their coupling with disk gas, which governs their motions in protoplanetary disks. Collisional outcomes also depend on geometric cross sections of initial aggregates. In a previous paper, we performed three-dimensional N-body simulations of sequential collisions of aggregates composed of a number of sub-micron-sized icy particles and examined radii of gyration (and bulk densities) of the obtained aggregates. We showed that collisional compression of aggregates is not efficient and that aggregates remain fluffy. In the present study, we examine geometric cross sections of the aggregates. Their cross sections decrease due to compression as wellmore » as to their gyration radii. It is found that a relation between the cross section and the gyration radius proposed by Okuzumi et al. is valid for the compressed aggregates. We also refine the compression model proposed in our previous paper. The refined model enables us to calculate the evolution of both gyration radii and cross sections of growing aggregates and reproduces well our numerical results of sequential aggregate collisions. The refined model can describe non-equal-mass collisions as well as equal-mass cases. Although we do not take into account oblique collisions in the present study, oblique collisions would further hinder compression of aggregates.« less

Defining and systematic analyses of aggregation indices to evaluate degree of calcium oxalate crystal aggregation

NASA Astrophysics Data System (ADS)

Chaiyarit, Sakdithep; Thongboonkerd, Visith

2017-12-01

Crystal aggregation is one of the most crucial steps in kidney stone pathogenesis. However, previous studies of crystal aggregation were rarely done and quantitative analysis of aggregation degree was handicapped by a lack of the standard measurement. We thus performed an in vitro assay to generate aggregation of calcium oxalate monohydrate (COM) crystals with various concentrations (25-800 µg/ml) in saturated aggregation buffer. The crystal aggregates were analyzed by microscopic examination, UV-visible spectrophotometry, and GraphPad Prism6 software to define a total of 12 aggregation indices (including number of aggregates, aggregated mass index, optical density, aggregation coefficient, span, number of aggregates at plateau time-point, aggregated area index, aggregated diameter index, aggregated symmetry index, time constant, half-life, and rate constant). The data showed linear correlation between crystal concentration and almost all of these indices, except only for rate constant. Among these, number of aggregates provided the greatest regression coefficient (r=0.997; p<0.001), whereas the equally second rank included aggregated mass index and optical density (r=0.993; p<0.001 and r=‑0.993; p<0.001, respectively) and the equally forth were aggregation coefficient and span (r=0.991; p<0.001 for both). These five indices are thus recommended as the most appropriate indices for quantitative analysis of COM crystal aggregation in vitro.

Sustainable aggregates production : green applications for aggregate by-products.

DOT National Transportation Integrated Search

2015-06-01

Increased emphasis in the construction industry on sustainability and recycling requires production of : aggregate gradations with lower dust (cleaner aggregates) and smaller maximum sizeshence, increased : amount of quarry by-products (QBs). QBs ...

Thermodynamics of Protein Aggregation

NASA Astrophysics Data System (ADS)

Osborne, Kenneth L.; Barz, Bogdan; Bachmann, Michael; Strodel, Birgit

Amyloid protein aggregation characterizes many neurodegenerative disorders, including Alzheimer's, Parkinson's, and Creutz- feldt-Jakob disease. Evidence suggests that amyloid aggregates may share similar aggregation pathways, implying simulation of full-length amyloid proteins is not necessary for understanding amyloid formation. In this study we simulate GNNQQNY, the N-terminal prion-determining domain of the yeast protein Sup35 to investigate the thermodynamics of structural transitions during aggregation. We use a coarse-grained model with replica-exchange molecular dynamics to investigate the association of 3-, 6-, and 12-chain GNNQQNY systems and we determine the aggregation pathway by studying aggregation states of GN- NQQNY. We find that the aggregation of the hydrophilic GNNQQNY sequence is mainly driven by H-bond formation, leading to the formation of /3-sheets from the very beginning of the assembly process. Condensation (aggregation) and ordering take place simultaneously, which is underpinned by the occurrence of a single heat capacity peak only.

Microbial characterization of nitrification in a shallow, nitrogen-contaminated aquifer, Cape Cod, Massachusetts and detection of a novel cluster associated with nitrifying Betaproteobacteria

NASA Astrophysics Data System (ADS)

Miller, Daniel N.; Smith, Richard L.

2009-01-01

Groundwater nitrification is a poorly characterized process affecting the speciation and transport of nitrogen. Cores from two sites in a plume of contamination were examined using culture-based and molecular techniques targeting nitrification processes. The first site, located beneath a sewage effluent infiltration bed, received treated effluent containing O 2 (> 300 µM) and NH 4+ (51-800 µM). The second site was 2.5 km down-gradient near the leading edge of the ammonium zone within the contaminant plume and featured vertical gradients of O 2, NH 4+, and NO 3- (0-300, 0-500, and 100-200 µM with depth, respectively). Ammonia- and nitrite-oxidizers enumerated by the culture-based MPN method were low in abundance at both sites (1.8 to 350 g - 1 and 33 to 35,000 g - 1 , respectively). Potential nitrifying activity measured in core material in the laboratory was also very low, requiring several weeks for products to accumulate. Molecular analysis of aquifer DNA (nested PCR followed by cloning and 16S rDNA sequencing) detected primarily sequences associated with the Nitrosospira genus throughout the cores at the down-gradient site and a smaller proportion from the Nitrosomonas genus in the deeper anoxic, NH 4+ zone at the down-gradient site. Only a single Nitrosospira sequence was detected beneath the infiltration bed. Furthermore, the majority of Nitrosospira-associated sequences represent an unrecognized cluster. We conclude that an uncharacterized group associated with Nitrosospira dominate at the geochemically stable, down-gradient site, but found little evidence for Betaproteobacteria nitrifiers beneath the infiltration beds where geochemical conditions were more variable.

Neuroforecasting Aggregate Choice

PubMed Central

Knutson, Brian; Genevsky, Alexander

2018-01-01

Advances in brain-imaging design and analysis have allowed investigators to use neural activity to predict individual choice, while emerging Internet markets have opened up new opportunities for forecasting aggregate choice. Here, we review emerging research that bridges these levels of analysis by attempting to use group neural activity to forecast aggregate choice. A survey of initial findings suggests that components of group neural activity might forecast aggregate choice, in some cases even beyond traditional behavioral measures. In addition to demonstrating the plausibility of neuroforecasting, these findings raise the possibility that not all neural processes that predict individual choice forecast aggregate choice to the same degree. We propose that although integrative choice components may confer more consistency within individuals, affective choice components may generalize more broadly across individuals to forecast aggregate choice. PMID:29706726

Patterns of [PSI+] aggregation allow insights into cellular organization of yeast prion aggregates

PubMed Central

Tyedmers, Jens

2012-01-01

The yeast prion phenomenon is very widespread and mounting evidence suggests that it has an impact on cellular regulatory mechanisms related to phenotypic responses to changing environments. Studying the aggregation patterns of prion amyloids during different stages of the prion life cycle is a first key step to understand major principles of how and where cells generate, organize and turn-over prion aggregates. The induction of the [PSI+] state involves the actin cytoskeleton and quality control compartments such as the Insoluble Protein Deposit (IPOD). An initially unstable transitional induction state can be visualized by overexpression of the prion determinant and displays characteristic large ring- and ribbon-shaped aggregates consisting of poorly fragmented bundles of very long prion fibrils. In the mature prion state, the aggregation pattern is characterized by highly fragmented, shorter prion fibrils that form aggregates, which can be visualized through tagging with fluorescent proteins. The number of aggregates formed varies, ranging from a single large aggregate at the IPOD to multiple smaller ones, depending on several parameters discussed. Aggregate units below the resolution of light microscopy that are detectable by fluorescence correlation spectroscopy are in equilibrium with larger aggregates in this stage and can mediate faithful inheritance of the prion state. Loss of the prion state is often characterized by reduced fragmentation of prion fibrils and fewer, larger aggregates. PMID:22449721

Bacterial Extracellular Polysaccharides in Biofilm Formation and Function

PubMed Central

Limoli, Dominique H.; Jones, Christopher J.; Wozniak, Daniel J.

2015-01-01

Microbes produce a biofilm matrix consisting of proteins, extracellular DNA, and polysaccharides that is integral in the formation of bacterial communities. Historical studies of polysaccharides revealed that their overproduction often alters the colony morphology and can be diagnostic in identifying certain species. The polysaccharide component of the matrix can provide many diverse benefits to the cells in the biofilm, including adhesion, protection, and structure. Aggregative polysaccharides act as molecular glue, allowing the bacterial cells to adhere to each other as well as surfaces. Adhesion facilitates the colonization of both biotic and abiotic surfaces by allowing the bacteria to resist physical stresses imposed by fluid movement that could separate the cells from a nutrient source. Polysaccharides can also provide protection from a wide range of stresses, such as desiccation, immune effectors, and predators such as phagocytic cells and amoebae. Finally, polysaccharides can provide structure to biofilms, allowing stratification of the bacterial community and establishing gradients of nutrients and waste products. This can be advantageous for the bacteria by establishing a heterogeneous population that is prepared to endure stresses created by the rapidly changing environments that many bacteria encounter. The diverse range of polysaccharide structures, properties, and roles highlight the importance of this matrix constituent to the successful adaptation of bacteria to nearly every niche. Here, we present an overview of the current knowledge regarding the diversity and benefits that polysaccharide production provides to bacterial communities within biofilms. PMID:26185074

Bacterial Extracellular Polysaccharides in Biofilm Formation and Function.

PubMed

Limoli, Dominique H; Jones, Christopher J; Wozniak, Daniel J

2015-06-01

Microbes produce a biofilm matrix consisting of proteins, extracellular DNA, and polysaccharides that is integral in the formation of bacterial communities. Historical studies of polysaccharides revealed that their overproduction often alters the colony morphology and can be diagnostic in identifying certain species. The polysaccharide component of the matrix can provide many diverse benefits to the cells in the biofilm, including adhesion, protection, and structure. Aggregative polysaccharides act as molecular glue, allowing the bacterial cells to adhere to each other as well as surfaces. Adhesion facilitates the colonization of both biotic and abiotic surfaces by allowing the bacteria to resist physical stresses imposed by fluid movement that could separate the cells from a nutrient source. Polysaccharides can also provide protection from a wide range of stresses, such as desiccation, immune effectors, and predators such as phagocytic cells and amoebae. Finally, polysaccharides can provide structure to biofilms, allowing stratification of the bacterial community and establishing gradients of nutrients and waste products. This can be advantageous for the bacteria by establishing a heterogeneous population that is prepared to endure stresses created by the rapidly changing environments that many bacteria encounter. The diverse range of polysaccharide structures, properties, and roles highlight the importance of this matrix constituent to the successful adaptation of bacteria to nearly every niche. Here, we present an overview of the current knowledge regarding the diversity and benefits that polysaccharide production provides to bacterial communities within biofilms.

Non-Arrhenius protein aggregation.

PubMed

Wang, Wei; Roberts, Christopher J

2013-07-01

Protein aggregation presents one of the key challenges in the development of protein biotherapeutics. It affects not only product quality but also potentially impacts safety, as protein aggregates have been shown to be linked with cytotoxicity and patient immunogenicity. Therefore, investigations of protein aggregation remain a major focus in pharmaceutical companies and academic institutions. Due to the complexity of the aggregation process and temperature-dependent conformational stability, temperature-induced protein aggregation is often non-Arrhenius over even relatively small temperature windows relevant for product development, and this makes low-temperature extrapolation difficult based simply on accelerated stability studies at high temperatures. This review discusses the non-Arrhenius nature of the temperature dependence of protein aggregation, explores possible causes, and considers inherent hurdles for accurately extrapolating aggregation rates from conventional industrial approaches for selecting accelerated conditions and from conventional or more advanced methods of analyzing the resulting rate data.

Effect of aggregate graining compositions on skid resistance of Exposed Aggregate Concrete pavement

NASA Astrophysics Data System (ADS)

Wasilewska, Marta; Gardziejczyk, Wladysław; Gierasimiuk, Pawel

2018-05-01

The paper presents the evaluation of skid resistance of EAC (Exposed Aggregate Concrete) pavements which differ in aggregate graining compositions. The tests were carried out on concrete mixes with a maximum aggregate size of 8 mm. Three types of coarse aggregates were selected depending on their resistance to polishing which was determined on the basis of the PSV (Polished Stone Value). Basalt (PSV 48), gabbro (PSV 50) and trachybasalt (PSV 52) aggregates were chosen. For each type of aggregate three graining compositions were designed, which differed in the content of coarse aggregate > 4mm. Their content for each series was as follows: A - 38%, B - 50% and C - 68%. Evaluation of the skid resistance has been performed using the FAP (Friction After Polishing) test equipment also known as the Wehner/Schulze machine. Laboratory method enables to compare the skid resistance of different types of wearing course under specified conditions simulating polishing processes. In addition, macrotexture measurements were made on the surface of each specimen using the Elatexure laser profile. Analysis of variance showed that at significance level α = 0.05, aggregate graining compositions as well as the PSV have a significant influence on the obtained values of the friction coefficient μm of the tested EAC pavements. The highest values of the μm have been obtained for EAC with the lowest amount of coarse aggregates (compositions A). In these cases the resistance to polishing of the aggregate does not significantly affect the friction coefficients. This is related to the large areas of cement mortar between the exposed coarse grains. Based on the analysis of microscope images, it was observed that the coarse aggregates were not sufficiently exposed. It has been proved that PSV significantly affected the coefficient of friction in the case of compositions B and C. This is caused by large areas of exposed coarse aggregate. The best parameters were achieved for the EAC pavements

Inhibitory effect of cyanide on wastewater nitrification determined using SOUR and RNA-based gene-specific assays.

PubMed

Kapoor, V; Elk, M; Li, X; Santo Domingo, J W

2016-08-01

The effect of cyanide (CN(-) ) on nitrification was examined with samples from nitrifying bacterial enrichments using two different approaches: by measuring substrate (ammonia) specific oxygen uptake rates (SOUR), and by using RT-qPCR to quantify the transcripts of functional genes involved in nitrification. The nitrifying bioreactor was operated as a continuous reactor with a 24 h hydraulic retention time. The samples were exposed in batch vessels to cyanide for a period of 12 h. The concentrations of CN(-) used in the batch assays were 0·03, 0·06, 0·1 and 1·0 mg l(-1) . There was considerable decrease in SOUR with increasing dosages of CN(-) . A decrease of more than 50% in nitrification activity was observed at 0·1 mg l(-1) CN(-) . Based on the RT-qPCR data, there was notable reduction in the transcript levels of amoA and hao for increasing CN(-) dosage, which corresponded well with the ammonia oxidation activity measured via SOUR. The inhibitory effect of cyanide may be attributed to the affinity of cyanide to bind ferric haeme proteins, which disrupt protein structure and function. The correspondence between the relative expression of functional genes and SOUR shown in this study demonstrates the efficacy of RNA-based function-specific assays for better understanding of the effect of toxic compounds on nitrification activity in wastewater. The effect of cyanide on nitrifying bacteria was characterized by measuring physiological and transcriptional response. Cyanide was inhibitory to nitrification at concentrations that may be found in industrial waste. The RNA-based function-specific assays represent a mechanistic approach for better understanding the effect of toxic compounds on nitrification activity in wastewater. Moreover, the relative abundance of RNA transcripts can be used to closely track in situ nitrifying bacterial activity which can be used to predict inhibition events, thereby providing a metric to potentially improve performance of

Evaluation of Canadian unconfined aggregate freeze-thaw tests for identifying nondurable aggregates.

DOT National Transportation Integrated Search

2012-06-01

Concrete is the most widely used material in construction. Aggregates contribute 60% to 75% of the total volume : of concrete. The aggregates play a key role in concrete durability. The U.S. Midwest has many aggregates that can : show distress in the...

Bartonella henselae engages inside-out and outside-in signaling by integrin β1 and talin1 during invasome-mediated bacterial uptake.

PubMed

Truttmann, Matthias C; Misselwitz, Benjamin; Huser, Sonja; Hardt, Wolf-Dietrich; Critchley, David R; Dehio, Christoph

2011-11-01

The VirB/D4 type IV secretion system (T4SS) of the bacterial pathogen Bartonella henselae (Bhe) translocates seven effector proteins (BepA-BepG) into human cells that subvert host cellular functions. Two redundant pathways dependent on BepG or the combination of BepC and BepF trigger the formation of a bacterial uptake structure termed the invasome. Invasome formation is a multi-step process consisting of bacterial adherence, effector translocation, aggregation of bacteria on the cell surface and engulfment, and eventually, complete internalization of the bacterial aggregate occurs in an F-actin-dependent manner. In the present study, we show that Bhe-triggered invasome formation depends on integrin-β1-mediated signaling cascades that enable assembly of the F-actin invasome structure. We demonstrate that Bhe interacts with integrin β1 in a fibronectin- and VirB/D4 T4SS-independent manner and that activated integrin β1 is essential for both effector translocation and the actin rearrangements leading to invasome formation. Furthermore, we show that talin1, but not talin2, is required for inside-out activation of integrin β1 during invasome formation. Finally, integrin-β1-mediated outside-in signaling by FAK, Src, paxillin and vinculin is necessary for invasome formation. This is the first example of a bacterial entry process that fully exploits the bi-directional signaling capacity of integrin receptors in a talin1-specific manner.

Simultaneous measurement of the viability, aggregation, and live and dead adherence of Streptococcus crista, Streptococcus mutans and Actinobacillus actinomycetemcomitans in human saliva in relation to indices of caries, dental plaque and periodontal disease.

PubMed

Rudney, J D; Staikov, R K

2002-05-01

Salivary proteins have multiple functions and many share similar functions, which may be why it has been difficult to relate variations in their concentrations to oral health and ecology. An alternative is to focus on variations in the major functions of saliva. An hydroxyapatite-coated microplate model has been developed that simultaneously measures saliva-promoted bacterial viability, bacterial aggregation, and live and dead bacterial adherence, while simulating oral temperature and shearing forces from swallowing. That model was applied to resting whole and stimulated parotid saliva from 149 individuals, using representative strains of Streptococcus crista, S. mutans, and Actinobacillus actinomycetemcomitans. Two major factors were defined by multivariate analysis (this was successful only for whole-saliva). One factor was correlated with aggregation, live adherence and dead adherence for all three strains; the other was correlated with total viability of all three strains. Participants were grouped <25th percentile and >75th percentile for each factor. Those groups were compared for clinical indices of oral health. Caries scores were significantly lower in those with high scores for aggregation-adherence, regardless of whether total viability scores were low or high. Live bacteria always predominated on surfaces when live and dead adherence scores were expressed as ratios. However, participants with high scores for aggregation-adherence showed significantly more dead adherent bacteria than those with low scores (these ratios were uncorrelated with total viability). This finding may indicate that extreme differences in the ability to kill bacteria on surfaces can influence caries risk.

Low nitrous oxide production through nitrifier-denitrification in intermittent-feed high-rate nitritation reactors.

PubMed

Su, Qingxian; Ma, Chun; Domingo-Félez, Carlos; Kiil, Anne Sofie; Thamdrup, Bo; Jensen, Marlene Mark; Smets, Barth F

2017-10-15

Nitrous oxide (N 2 O) production from autotrophic nitrogen conversion processes, especially nitritation systems, can be significant, requires understanding and calls for mitigation. In this study, the rates and pathways of N 2 O production were quantified in two lab-scale sequencing batch reactors operated with intermittent feeding and demonstrating long-term and high-rate nitritation. The resulting reactor biomass was highly enriched in ammonia-oxidizing bacteria, and converted ∼93 ± 14% of the oxidized ammonium to nitrite. The low DO set-point combined with intermittent feeding was sufficient to maintain high nitritation efficiency and high nitritation rates at 20-26 °C over a period of ∼300 days. Even at the high nitritation efficiencies, net N 2 O production was low (∼2% of the oxidized ammonium). Net N 2 O production rates transiently increased with a rise in pH after each feeding, suggesting a potential effect of pH on N 2 O production. In situ application of 15 N labeled substrates revealed nitrifier denitrification as the dominant pathway of N 2 O production. Our study highlights operational conditions that minimize N 2 O emission from two-stage autotrophic nitrogen removal systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

Multivariate relationships between microbial communities and environmental variables during co-composting of sewage sludge and agricultural waste in the presence of PVP-AgNPs.

PubMed

Zhang, Lihua; Zhang, Jiachao; Zeng, Guangming; Dong, Haoran; Chen, Yaoning; Huang, Chao; Zhu, Yuan; Xu, Rui; Cheng, Yujun; Hou, Kunjie; Cao, Weicheng; Fang, Wei

2018-08-01

This study evaluated the contributions of environmental variables to the variations in bacterial 16S rDNA, nitrifying and denitrifying genes abundances during composting in the presence of polyvinylpyrrolidone coated silver nanoparticles (PVP-AgNPs). Manual forward selection in redundancy analysis (RDA) indicated that the variation in 16S rDNA was significantly explained by NO 3 - -N, while nitrifying genes were significantly related with pH, and denitrifying genes were driven by NO 3 - -N and TN. Partial RDA further revealed that NO 3 - -N solely explained 28.8% of the variation in 16S rDNA abundance, and pH accounted for 61.8% of the variation in nitrifying genes. NO 3 - -N and TN accounted for 34.2% and 9.2% of denitrifying genes variation, respectively. The RDA triplots showed that different genes shared different relationships with environmental parameters. Based on these findings, a composting with high efficiency and quality may be conducted in the future work by adjusting the significant environmental variables. Copyright © 2018 Elsevier Ltd. All rights reserved.

Amyloid-beta aggregation: selective inhibition of aggregation in mixtures of amyloid with different chain lengths.

PubMed Central

Snyder, S W; Ladror, U S; Wade, W S; Wang, G T; Barrett, L W; Matayoshi, E D; Huffaker, H J; Krafft, G A; Holzman, T F

1994-01-01

One of the clinical manifestations of Alzheimer's disease is the deposition of the 39-43 residue amyloid-beta (A beta) peptide in aggregated fibrils in senile plaques. Characterization of the aggregation behavior of A beta is one of the critical issues in understanding the role of A beta in the disease process. Using solution hydrodynamics, A beta was observed to form three types of species in phosphate-buffered saline: insoluble aggregates with sedimentation coefficients of approximately 50,000 S and molecular masses of approximately 10(9) Da, "soluble aggregates" with sedimentation coefficients of approximately 30 S and masses of approximately 10(6) Da, and monomer. When starting from monomer, the aggregation kinetics of A beta 1-40 (A beta 40) and A beta 1-42 (A beta 42), alone and in combination, reveal large differences in the tendency of these peptides to aggregate as a function of pH and other solution conditions. At pH 4.1 and 7.0-7.4, aggregation is significantly slower than at pH 5 and 6. Under all conditions, aggregation of the longer A beta 42 was more rapid than A beta 40. Oxidation of Met-35 to the sulfoxide in A beta 40 enhances the aggregation rate over that of the nonoxidized peptide. Aggregation was found to be dependent upon temperature and to be strongly dependent on peptide concentration and ionic strength, indicating that aggregation is driven by a hydrophobic effect. When A beta 40 and A beta 42 are mixed together, A beta 40 retards the aggregation of A beta 42 in a concentration-dependent manner. Shorter fragments have a decreasing ability to interfere with A beta 42 aggregation. Conversely, the rate of aggregation of A beta 40 can be significantly enhanced by seeding slow aggregating solutions with preformed aggregates of A beta 42. Taken together, the inhibition of A beta 42 aggregation by A beta 40, the seeding of A beta 40 aggregation by A beta 42 aggregates, and the chemical oxidation of A beta 40 suggest that the relative abundance and

Multiple Functional Domains of Enterococcus faecalis Aggregation Substance Asc10 Contribute to Endocarditis Virulence ▿ †

PubMed Central

Chuang, Olivia N.; Schlievert, Patrick M.; Wells, Carol L.; Manias, Dawn A.; Tripp, Timothy J.; Dunny, Gary M.

2009-01-01

Aggregation substance proteins encoded by sex pheromone plasmids increase the virulence of Enterococcus faecalis in experimental pathogenesis models, including infectious endocarditis models. These large surface proteins may contain multiple functional domains involved in various interactions with other bacterial cells and with the mammalian host. Aggregation substance Asc10, encoded by plasmid pCF10, is induced during growth in the mammalian bloodstream, and pCF10 carriage gives E. faecalis a significant selective advantage in this environment. We employed a rabbit model to investigate the role of various functional domains of Asc10 in endocarditis. The data suggested that the bacterial load of the infected tissue was the best indicator of virulence. Isogenic strains carrying either no plasmid, wild-type pCF10, a pCF10 derivative with an in-frame deletion of the prgB gene encoding Asc10, or pCF10 derivatives expressing other alleles of prgB were examined in this model. Previously identified aggregation domains contributed to the virulence associated with the wild-type protein, and a strain expressing an Asc10 derivative in which glycine residues in two RGD motifs were changed to alanine residues showed the greatest reduction in virulence. Remarkably, this strain and the strain carrying the pCF10 derivative with the in-frame deletion of prgB were both significantly less virulent than an isogenic plasmid-free strain. The data demonstrate that multiple functional domains are important in Asc10-mediated interactions with the host during the course of experimental endocarditis and that in the absence of a functional prgB gene, pCF10 carriage is actually disadvantageous in vivo. PMID:18955479

Ecosystem Resilience and Limitations Revealed by Soil Bacterial Community Dynamics in a Bark Beetle-Impacted Forest

DOE PAGES

Mikkelson, Kristin M.; Brouillard, Brent M.; Bokman, Chelsea M.; ...

2017-12-05

ABSTRACT Forested ecosystems throughout the world are experiencing increases in the incidence and magnitude of insect-induced tree mortality with large ecologic ramifications. Interestingly, correlations between water quality and the extent of tree mortality in Colorado montane ecosystems suggest compensatory effects from adjacent live vegetation that mute responses in less severely impacted forests. To this end, we investigated whether the composition of the soil bacterial community and associated functionality beneath beetle-killed lodgepole pine was influenced by the extent of surrounding tree mortality. The most pronounced changes were observed in the potentially active bacterial community, where alpha diversity increased in concert withmore » surrounding tree mortality until mortality exceeded a tipping point of ~30 to 40%, after which diversity stabilized and decreased. Community structure also clustered in association with the extent of surrounding tree mortality with compositional trends best explained by differences in NH 4 + concentrations and C/N ratios. C/N ratios, which were lower in soils under beetle-killed trees, further correlated with the relative abundance of putative nitrifiers and exoenzyme activity. Collectively, the response of soil microorganisms that drive heterotrophic respiration and decay supports observations of broader macroscale threshold effects on water quality in heavily infested forests and could be utilized as a predictive mechanism during analogous ecosystem disruptions. IMPORTANCE Forests around the world are succumbing to insect infestation with repercussions for local soil biogeochemistry and downstream water quality and quantity. This study utilized microbial community dynamics to address why we are observing watershed scale biogeochemical impacts from forest mortality in some impacted areas but not others. Through a unique “tree-centric” approach, we were able to delineate plots with various tree mortality levels

Ecosystem Resilience and Limitations Revealed by Soil Bacterial Community Dynamics in a Bark Beetle-Impacted Forest.

PubMed

Mikkelson, Kristin M; Brouillard, Brent M; Bokman, Chelsea M; Sharp, Jonathan O

2017-12-05

Forested ecosystems throughout the world are experiencing increases in the incidence and magnitude of insect-induced tree mortality with large ecologic ramifications. Interestingly, correlations between water quality and the extent of tree mortality in Colorado montane ecosystems suggest compensatory effects from adjacent live vegetation that mute responses in less severely impacted forests. To this end, we investigated whether the composition of the soil bacterial community and associated functionality beneath beetle-killed lodgepole pine was influenced by the extent of surrounding tree mortality. The most pronounced changes were observed in the potentially active bacterial community, where alpha diversity increased in concert with surrounding tree mortality until mortality exceeded a tipping point of ~30 to 40%, after which diversity stabilized and decreased. Community structure also clustered in association with the extent of surrounding tree mortality with compositional trends best explained by differences in NH 4 + concentrations and C/N ratios. C/N ratios, which were lower in soils under beetle-killed trees, further correlated with the relative abundance of putative nitrifiers and exoenzyme activity. Collectively, the response of soil microorganisms that drive heterotrophic respiration and decay supports observations of broader macroscale threshold effects on water quality in heavily infested forests and could be utilized as a predictive mechanism during analogous ecosystem disruptions. IMPORTANCE Forests around the world are succumbing to insect infestation with repercussions for local soil biogeochemistry and downstream water quality and quantity. This study utilized microbial community dynamics to address why we are observing watershed scale biogeochemical impacts from forest mortality in some impacted areas but not others. Through a unique "tree-centric" approach, we were able to delineate plots with various tree mortality levels within the same watershed

Ecosystem Resilience and Limitations Revealed by Soil Bacterial Community Dynamics in a Bark Beetle-Impacted Forest

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mikkelson, Kristin M.; Brouillard, Brent M.; Bokman, Chelsea M.

ABSTRACT Forested ecosystems throughout the world are experiencing increases in the incidence and magnitude of insect-induced tree mortality with large ecologic ramifications. Interestingly, correlations between water quality and the extent of tree mortality in Colorado montane ecosystems suggest compensatory effects from adjacent live vegetation that mute responses in less severely impacted forests. To this end, we investigated whether the composition of the soil bacterial community and associated functionality beneath beetle-killed lodgepole pine was influenced by the extent of surrounding tree mortality. The most pronounced changes were observed in the potentially active bacterial community, where alpha diversity increased in concert withmore » surrounding tree mortality until mortality exceeded a tipping point of ~30 to 40%, after which diversity stabilized and decreased. Community structure also clustered in association with the extent of surrounding tree mortality with compositional trends best explained by differences in NH 4 + concentrations and C/N ratios. C/N ratios, which were lower in soils under beetle-killed trees, further correlated with the relative abundance of putative nitrifiers and exoenzyme activity. Collectively, the response of soil microorganisms that drive heterotrophic respiration and decay supports observations of broader macroscale threshold effects on water quality in heavily infested forests and could be utilized as a predictive mechanism during analogous ecosystem disruptions. IMPORTANCE Forests around the world are succumbing to insect infestation with repercussions for local soil biogeochemistry and downstream water quality and quantity. This study utilized microbial community dynamics to address why we are observing watershed scale biogeochemical impacts from forest mortality in some impacted areas but not others. Through a unique “tree-centric” approach, we were able to delineate plots with various tree mortality levels

A Novel Method to Quantify Soil Aggregate Stability by Measuring Aggregate Bond Energies

NASA Astrophysics Data System (ADS)

Efrat, Rachel; Rawlins, Barry G.; Quinton, John N.; Watts, Chris W.; Whitmore, Andy P.

2016-04-01

Soil aggregate stability is a key indicator of soil quality because it controls physical, biological and chemical functions important in cultivated soils. Micro-aggregates are responsible for the long term sequestration of carbon in soil, therefore determine soils role in the carbon cycle. It is thus vital that techniques to measure aggregate stability are accurate, consistent and reliable, in order to appropriately manage and monitor soil quality, and to develop our understanding and estimates of soil as a carbon store to appropriately incorporate in carbon cycle models. Practices used to assess the stability of aggregates vary in sample preparation, operational technique and unit of results. They use proxies and lack quantification. Conflicting results are therefore drawn between projects that do not provide methodological or resultant comparability. Typical modern stability tests suspend aggregates in water and monitor fragmentation upon exposure to an un-quantified amount of ultrasonic energy, utilising a laser granulometer to measure the change in mean weight diameter. In this project a novel approach has been developed based on that of Zhu et al., (2009), to accurately quantify the stability of aggregates by specifically measuring their bond energies. The bond energies are measured operating a combination of calorimetry and a high powered ultrasonic probe, with computable output function. Temperature change during sonication is monitored by an array of probes which enables calculation of the energy spent heating the system (Ph). Our novel technique suspends aggregates in heavy liquid lithium heteropolytungstate, as opposed to water, to avoid exposing aggregates to an immeasurable disruptive energy source, due to cavitation, collisions and clay swelling. Mean weight diameter is measured by a laser granulometer to monitor aggregate breakdown after successive periods of calculated ultrasonic energy input (Pi), until complete dispersion is achieved and bond

N-Acetyl-L-cysteine Effects on Multi-species Oral Biofilm Formation and Bacterial Ecology

PubMed Central

Rasmussen, Karin; Nikrad, Julia; Reilly, Cavan; Li, Yuping; Jones, Robert S.

2015-01-01

Future therapies for the treatment of dental decay have to consider the importance of preserving bacterial ecology while reducing biofilm adherence to teeth. A multi-species plaque derived (MSPD) biofilm model was used to assess how concentrations of N-acetyl-L-cysteine (0, 0.1%, 1%, 10%) affected the growth of complex oral biofilms. Biofilms were grown (n=96) for 24 hours on hydroxyapatite disks in BMM media with 0.5% sucrose. Bacterial viability and biomass formation was examined on each disk using a microtiter plate reader. In addition, fluorescence microscopy and Scanning Electron Microscopy was used to qualitatively examine the effect of NAC on bacterial biofilm aggregation, extracellular components, and bacterial morphology. The total biomass was significantly decreased after exposure of both 1% (from 0.48, with a 95% confidence interval of (0.44, 0.57) to 0.35, with confidence interval (0.31, 0.38)) and 10% NAC (0.14 with confidence interval (0.11, 0.17)). 16S rRNA amplicon sequencing analysis indicated that 1% NAC reduced biofilm adherence while preserving biofilm ecology. PMID:26518358

Curcumin Attenuates Amyloid-β Aggregate Toxicity and Modulates Amyloid-β Aggregation Pathway.

PubMed

Thapa, Arjun; Jett, Stephen D; Chi, Eva Y

2016-01-20

The abnormal misfolding and aggregation of amyloid-β (Aβ) peptides into β-sheet enriched insoluble deposits initiates a cascade of events leading to pathological processes and culminating in cognitive decline in Alzheimer's disease (AD). In particular, soluble oligomeric/prefibrillar Aβ have been shown to be potent neurotoxins. The naturally occurring polyphenol curcumin has been shown to exert a neuroprotective effect against age-related neurodegenerative diseases such as AD. However, its protective mechanism remains unclear. In this study, we investigated the effects of curcumin on the aggregation of Aβ40 as well as Aβ40 aggregate induced neurotoxicity. Our results show that the curcumin does not inhibit Aβ fibril formation, but rather enriches the population of "off-pathway" soluble oligomers and prefibrillar aggregates that were nontoxic. Curcumin also exerted a nonspecific neuroprotective effect, reducing toxicities induced by a range of Aβ conformers, including monomeric, oligomeric, prefibrillar, and fibrillar Aβ. The neuroprotective effect is possibly membrane-mediated, as curcumin reduced the extent of cell membrane permeabilization induced by Aβ aggregates. Taken together, our study shows that curcumin exerts its neuroprotective effect against Aβ induced toxicity through at least two concerted pathways, modifying the Aβ aggregation pathway toward the formation of nontoxic aggregates and ameliorating Aβ-induced toxicity possibly through a nonspecific pathway.

Effect of disinfectant, water age, and pipe materials on bacterial and eukaryotic community structure in drinking water biofilm.

PubMed

Wang, Hong; Masters, Sheldon; Edwards, Marc A; Falkinham, Joseph O; Pruden, Amy

2014-01-01

Availability of safe, pathogen-free drinking water is vital to public health; however, it is impossible to deliver sterile drinking water to consumers. Recent microbiome research is bringing new understanding to the true extent and diversity of microbes that inhabit water distribution systems. The purpose of this study was to determine how water chemistry in main distribution lines shape the microbiome in drinking water biofilms and to explore potential associations between opportunistic pathogens and indigenous drinking water microbes. Effects of disinfectant (chloramines, chlorine), water age (2.3 days, 5.7 days), and pipe material (cement, iron, PVC) were compared in parallel triplicate simulated water distribution systems. Pyrosequencing was employed to characterize bacteria and terminal restriction fragment polymorphism was used to profile both bacteria and eukaryotes inhabiting pipe biofilms. Disinfectant and water age were both observed to be strong factors in shaping bacterial and eukaryotic community structures. Pipe material only influenced the bacterial community structure (ANOSIM test, P < 0.05). Interactive effects of disinfectant, pipe material, and water age on both bacteria and eukaryotes were noted. Disinfectant concentration had the strongest effect on bacteria, while dissolved oxygen appeared to be a major driver for eukaryotes (BEST test). Several correlations of similarity metrics among populations of bacteria, eukaryotes, and opportunistic pathogens, as well as one significant association between mycobacterial and proteobacterial operational taxonomic units, provides insight into means by which manipulating the microbiome may lead to new avenues for limiting the growth of opportunistic pathogens (e.g., Legionella) or other nuisance organisms (e.g., nitrifiers).

Consolidation of archaeological gypsum plaster by bacterial biomineralization of calcium carbonate.

PubMed

Jroundi, Fadwa; Gonzalez-Muñoz, Maria Teresa; Garcia-Bueno, Ana; Rodriguez-Navarro, Carlos

2014-09-01

Gypsum plasterworks and decorative surfaces are easily degraded, especially when exposed to humidity, and thus they require protection and/or consolidation. However, the conservation of historical gypsum-based structural and decorative materials by conventional organic and inorganic consolidants shows limited efficacy. Here, a new method based on the bioconsolidation capacity of carbonatogenic bacteria inhabiting the material was assayed on historical gypsum plasters and compared with conventional consolidation treatments (ethyl silicate; methylacrylate-ethylmethacrylate copolymer and polyvinyl butyral). Conventional products do not reach in-depth consolidation, typically forming a thin impervious surface layer which blocks pores. In contrast, the bacterial treatment produces vaterite (CaCO3) biocement, which does not block pores and produces a good level of consolidation, both at the surface and in-depth, as shown by drilling resistance measurement system analyses. Transmission electron microscopy analyses show that bacterial vaterite cement formed via oriented aggregation of CaCO3 nanoparticles (∼20nm in size), resulting in mesocrystals which incorporate bacterial biopolymers. Such a biocomposite has superior mechanical properties, thus explaining the fact that drilling resistance of bioconsolidated gypsum plasters is within the range of inorganic calcite materials of equivalent porosity, despite the fact that the bacterial vaterite cement accounts for only a 0.02 solid volume fraction. Bacterial bioconsolidation is proposed for the effective consolidation of this type of material. The potential applications of bacterial calcium carbonate consolidation of gypsum biomaterials used as bone graft substitutes are discussed. Copyright © 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Proteins aggregation and human diseases

NASA Astrophysics Data System (ADS)

Hu, Chin-Kun

2015-04-01

Many human diseases and the death of most supercentenarians are related to protein aggregation. Neurodegenerative diseases include Alzheimer's disease (AD), Huntington's disease (HD), Parkinson's disease (PD), frontotemporallobar degeneration, etc. Such diseases are due to progressive loss of structure or function of neurons caused by protein aggregation. For example, AD is considered to be related to aggregation of Aβ40 (peptide with 40 amino acids) and Aβ42 (peptide with 42 amino acids) and HD is considered to be related to aggregation of polyQ (polyglutamine) peptides. In this paper, we briefly review our recent discovery of key factors for protein aggregation. We used a lattice model to study the aggregation rates of proteins and found that the probability for a protein sequence to appear in the conformation of the aggregated state can be used to determine the temperature at which proteins can aggregate most quickly. We used molecular dynamics and simple models of polymer chains to study relaxation and aggregation of proteins under various conditions and found that when the bending-angle dependent and torsion-angle dependent interactions are zero or very small, then protein chains tend to aggregate at lower temperatures. All atom models were used to identify a key peptide chain for the aggregation of insulin chains and to find that two polyQ chains prefer anti-parallel conformation. It is pointed out that in many cases, protein aggregation does not result from protein mis-folding. A potential drug from Chinese medicine was found for Alzheimer's disease.

Two decades of warming increases diversity of a potentially lignolytic bacterial community

PubMed Central

Pold, Grace; Melillo, Jerry M.; DeAngelis, Kristen M.

2015-01-01

As Earth's climate warms, the massive stores of carbon found in soil are predicted to become depleted, and leave behind a smaller carbon pool that is less accessible to microbes. At a long-term forest soil-warming experiment in central Massachusetts, soil respiration and bacterial diversity have increased, while fungal biomass and microbially-accessible soil carbon have decreased. Here, we evaluate how warming has affected the microbial community's capability to degrade chemically-complex soil carbon using lignin-amended BioSep beads. We profiled the bacterial and fungal communities using PCR-based methods and completed extracellular enzyme assays as a proxy for potential community function. We found that lignin-amended beads selected for a distinct community containing bacterial taxa closely related to known lignin degraders, as well as members of many genera not previously noted as capable of degrading lignin. Warming tended to drive bacterial community structure more strongly in the lignin beads, while the effect on the fungal community was limited to unamended beads. Of those bacterial operational taxonomic units (OTUs) enriched by the warming treatment, many were enriched uniquely on lignin-amended beads. These taxa may be contributing to enhanced soil respiration under warming despite reduced readily available C availability. In aggregate, these results suggest that there is genetic potential for chemically complex soil carbon degradation that may lead to extended elevated soil respiration with long-term warming. PMID:26042112

Composition and Dynamics of Bacterial Communities of a Drinking Water Supply System as Assessed by RNA- and DNA-Based 16S rRNA Gene Fingerprinting

PubMed Central

Eichler, Stefan; Christen, Richard; Höltje, Claudia; Westphal, Petra; Bötel, Julia; Brettar, Ingrid; Mehling, Arndt; Höfle, Manfred G.

2006-01-01

Bacterial community dynamics of a whole drinking water supply system (DWSS) were studied from source to tap. Raw water for this DWSS is provided by two reservoirs with different water characteristics in the Harz mountains of Northern Germany. Samples were taken after different steps of treatment of raw water (i.e., flocculation, sand filtration, and chlorination) and at different points along the supply system to the tap. RNA and DNA were extracted from the sampled water. The 16S rRNA or its genes were partially amplified by reverse transcription-PCR or PCR and analyzed by single-strand conformation polymorphism community fingerprints. The bacterial community structures of the raw water samples from the two reservoirs were very different, but no major changes of these structures occurred after flocculation and sand filtration. Chlorination of the processed raw water strongly affected bacterial community structure, as reflected by the RNA-based fingerprints. This effect was less pronounced for the DNA-based fingerprints. After chlorination, the bacterial community remained rather constant from the storage containers to the tap. Furthermore, the community structure of the tap water did not change substantially for several months. Community composition was assessed by sequencing of abundant bands and phylogenetic analysis of the sequences obtained. The taxonomic compositions of the bacterial communities from both reservoirs were very different at the species level due to their different limnologies. On the other hand, major taxonomic groups, well known to occur in freshwater, such as Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes, were found in both reservoirs. Significant differences in the detection of the major groups were observed between DNA-based and RNA-based fingerprints irrespective of the reservoir. Chlorination of the drinking water seemed to promote growth of nitrifying bacteria. Detailed analysis of the community dynamics of the whole DWSS

Ecology of Nitrogen Fixing, Nitrifying, and Denitrifying Microorganisms in Tropical Forest Soils

PubMed Central

Pajares, Silvia; Bohannan, Brendan J. M.

2016-01-01

Soil microorganisms play important roles in nitrogen cycling within forest ecosystems. Current research has revealed that a wider variety of microorganisms, with unexpected diversity in their functions and phylogenies, are involved in the nitrogen cycle than previously thought, including nitrogen-fixing bacteria, ammonia-oxidizing bacteria and archaea, heterotrophic nitrifying microorganisms, and anammox bacteria, as well as denitrifying bacteria, archaea, and fungi. However, the vast majority of this research has been focused in temperate regions, and relatively little is known regarding the ecology of nitrogen-cycling microorganisms within tropical and subtropical ecosystems. Tropical forests are characterized by relatively high precipitation, low annual temperature fluctuation, high heterogeneity in plant diversity, large amounts of plant litter, and unique soil chemistry. For these reasons, regulation of the nitrogen cycle in tropical forests may be very different from that of temperate ecosystems. This is of great importance because of growing concerns regarding the effect of land use change and chronic-elevated nitrogen deposition on nitrogen-cycling processes in tropical forests. In the context of global change, it is crucial to understand how environmental factors and land use changes in tropical ecosystems influence the composition, abundance and activity of key players in the nitrogen cycle. In this review, we synthesize the limited currently available information regarding the microbial communities involved in nitrogen fixation, nitrification and denitrification, to provide deeper insight into the mechanisms regulating nitrogen cycling in tropical forest ecosystems. We also highlight the large gaps in our understanding of microbially mediated nitrogen processes in tropical forest soils and identify important areas for future research. PMID:27468277

Effects of maximum aggregate size on UPV of brick aggregate concrete.

PubMed

Mohammed, Tarek Uddin; Mahmood, Aziz Hasan

2016-07-01

Investigation was carried out to study the effects of maximum aggregate size (MAS) (12.5mm, 19.0mm, 25.0mm, 37.5mm, and 50.0mm) on ultrasonic pulse velocity (UPV) of concrete. For investigation, first class bricks were collected and broken to make coarse aggregate. The aggregates were tested for specific gravity, absorption capacity, unit weight, and abrasion resistance. Cylindrical concrete specimens were made with different sand to aggregate volume ratio (s/a) (0.40 and 0.45), W/C ratio (0.45, 0.50, and 0.55), and cement content (375kg/m(3) and 400kg/m(3)). The specimens were tested for compressive strength and Young's modulus. UPV through wet specimen was measured using Portable Ultrasonic Non-destructive Digital Indicating Tester (PUNDIT). Results indicate that the pulse velocity through concrete increases with an increase in MAS. Relationships between UPV and compressive strength; and UPV and Young's modulus of concrete are proposed for different maximum sizes of brick aggregate. Copyright © 2016 Elsevier B.V. All rights reserved.

Memantine inhibits β-amyloid aggregation and disassembles preformed β-amyloid aggregates.

PubMed

Takahashi-Ito, Kaori; Makino, Mitsuhiro; Okado, Keiko; Tomita, Taisuke

2017-11-04

Memantine, an uncompetitive glutamatergic N-methyl-d-aspartate (NMDA) receptor antagonist, is widely used as a medication for the treatment of Alzheimer's disease (AD). We previously reported that chronic treatment of AD with memantine reduces the amount of insoluble β-amyloid (Aβ) and soluble Aβ oligomers in animal models of AD. The mechanisms by which memantine reduces Aβ levels in the brain were evaluated by determining the effect of memantine on Aβ aggregation using thioflavin T and transmission electron microscopy. Memantine inhibited the formation of Aβ(1-42) aggregates in a concentration-dependent manner, whereas amantadine, a structurally similar compound, did not affect Aβ aggregation at the same concentrations. Furthermore, memantine inhibited the formation of different types of Aβ aggregates, including Aβs carrying familial AD mutations, and disaggregated preformed Aβ(1-42) fibrils. These results suggest that the inhibition of Aβ aggregation and induction of Aβ disaggregation may be involved in the mechanisms by which memantine reduces Aβ deposition in the brain. Copyright © 2017 Elsevier Inc. All rights reserved.

Oil-Price Shocks: Beyond Standard Aggregate Demand/Aggregate Supply Analysis.

ERIC Educational Resources Information Center

Elwood, S. Kirk

2001-01-01

Explores the problems of portraying oil-price shocks using the aggregate demand/aggregate supply model. Presents a simple modification of the model that differentiates between production and absorption of goods, which enables it to better reflect the effects of oil-price shocks on open economies. (RLH)

Metal concentrations in aggregate interiors, exteriors, whole aggregates, and bulk of Costa Rican soils

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilcke, W.; Kretzschmar, S.; Bundt, M.

1999-10-01

In many temperate soils the preferential weathering and leaching of aggregate surfaces and the nonaggregated material between aggregates depletes geogenic metals. It also shifts metals from strongly to more weakly bound metal forms. Deposited metals are sorbed preferentially on aggregate surfaces and between aggregates. The authors examined whether preferential desilication under tropical climate causes an enrichment in the aggregate exteriors in oxidic forms of metals. They also studied where deposited metals are bound in these soils. Aggregates (2--20 mm) were selected manually from the A horizons of eight Oxisols, six Andisols, two Mollisols, and two Inceptisols in Costa Rica. Allmore » samples were fractionated into interior and exterior portions and treated with a seven-step sequence to extract Al, Cd, Cu, Fe, Mn, Pb, and Zn. Total concentrations of all metals except Zn were higher in the aggregate exteriors than in the interiors. The average Cd and Pb concentrations in easily extractable fractions were significantly higher in the aggregate exteriors. There were no significant differences in metal partitioning between interiors and exteriors except for Pb, which had higher proportions in extractable forms with NH{sub 2}OH {center{underscore}dot} HCl {gt} NH{sub 4} - acetate, pH 6.0 {gt} EDTA in the exteriors. There were few significant differences in metal concentrations and partitioning between bulk soil and whole aggregates. The results may be explained by (i) preferential desilication of the aggregate exteriors and (ii) preferential sorption of deposited heavy metals mainly in easily extractable forms.« less

Soil quality and bacterial community structure: a case study from the mediterranean region

NASA Astrophysics Data System (ADS)

Anguita-Maeso, Manuel; Miralles*, Isabel; Soriano**, Miguel; Ortega, Raúl; García-Salcedo, José Antonio; Sánchez-Marañon, Manuel

2017-04-01

Bacterial communities play a central role in innumerable processes and functions of soils such as decomposition of organic residues, nutrient cycling, aggregation, and formation of humic substances. We investigated the relationships between bacterial communities, soil profiles, and quality parameters in eight benchmark soils of the Mediterranean calcareous mountain sampled on a local scale. The diversity and composition of prokaryotic community was assessed by 16S rRNA gene amplicon pyrosequencing of DNA from samples of topsoil (10 x 10 x 0.2 m). The bacterial profile content resulted in the identification of groups belonging to 16 phyla and 75 genera. Two-dimensional models using multidimensional scaling (Stress < 0.11), correspondence analysis (Inertia > 71%), and principal component analysis (Variance > 60%) showed a decrease in the abundance of acidobacteria Gp4 and Gp3 while actinobacteria flourished with increasing soil profile development (from Leptosol to Luvisol). This can be attributed to inherent changes in soil quality along pedogenesis such as pH (8.3 to 7.8), organic C (20.0 to 45.2 Mg ha-1), macropososity (0.11 to 0.32 cm3 cm-3), and water stable aggregates (365.8 to 963.4 Mg ha-1). Actinobacteria genera like Aciditerrimonas, Nocardioides, and Solirubrobacter also displayed positive correlations (r > 0.90) with the content of clay and free Ferric forms. Other factors like Re-carbonation, loss of organic matter, and soil compaction probably caused by land use and management, led to a decline in the Chao1 richness and Shannon diversity indices (3625 and 6.3) with respect to native soils (7852 and 7.4). Likewise, Firmicutes and Gemmatimonadetes were tripled and the genera of Proteobacteria and Bacteroidetes decreased. Our data indicate that bacterial community structure depends largely on the soil quality status, both inherent and managed and suggest the bacterial group composition also follows the course of soil genesis. (*) Financial support by Marie

Enzymatic biofilm digestion in soil aggregates facilitates the release of particulate organic matter by sonication

NASA Astrophysics Data System (ADS)

Büks, Frederick; Kaupenjohann, Martin

2016-10-01

The stability of soil aggregates against shearing and compressive forces as well as water-caused dispersion is an integral marker of soil quality. High stability results in less compaction and erosion and has been linked to enhanced water retention, dynamic water transport and aeration regimes, increased rooting depth, and protection of soil organic matter (SOM) against microbial degradation. In turn, particulate organic matter is supposed to support soil aggregate stabilization. For decades the importance of biofilm extracellular polymeric substances (EPSs) regarding particulate organic matter (POM) occlusion and aggregate stability has been canonical because of its distribution, geometric structure and ability to link primary particles. However, experimental proof is still missing. This lack is mainly due to methodological reasons. Thus, the objective of this work is to develop a method of enzymatic biofilm detachment for studying the effects of EPSs on POM occlusion. The method combines an enzymatic pre-treatment with different activities of α-glucosidase, β-galactosidase, DNAse and lipase with a subsequent sequential ultrasonic treatment for disaggregation and density fractionation of soils. POM releases of treated samples were compared to an enzyme-free control. To test the efficacy of biofilm detachment the ratio of bacterial DNA from suspended cells and the remaining biofilm after enzymatic treatment were measured by quantitative real-time PCR. Although the enzyme treatment was not sufficient for total biofilm removal, our results indicate that EPSs may attach POM within soil aggregates. The tendency to additional POM release with increased application of enzymes was attributed to a slight loss in aggregate stability. This suggests that an effect of agricultural practices on soil microbial populations could influence POM occlusion/aggregate stability and thereby carbon cycle/soil quality.

Impact of aerobic acclimation on the nitrification performance and microbial community of landfill leachate sludge.

PubMed

Hira, Daisuke; Aiko, Nobuyuki; Yabuki, Yoshinori; Fujii, Takao

2018-03-01

Nitrogenous pollution of water is regarded as a global environmental problem, and nitrogen removal has become an important issue in wastewater treatment processes. Landfill leachate is a typical large source of nitrogenous wastewater. Although the characteristics of leachate vary according to the age of the landfill, leachates of mature landfill have high concentrations of nitrogenous compounds. Most nitrogen in these leachates is in the form of ammonium nitrogen. In this study, we investigated the bacterial community of sludge from a landfill leachate lagoon by pyrosequencing of the bacterial 16S rRNA gene. The sludge was acclimated in a laboratory-scale reactor with aeration using a mechanical stirrer to promote nitrification. On 149 days, nitrification was achieved and then the bacterial community was also analyzed. The bacterial community was also analyzed after nitrification was achieved. Pyrosequencing analyses revealed that the abundances of ammonia-oxidizing and nitrite-oxidizing bacteria were increased by acclimation and their total proportions increased to >15% of total biomass. Changes in the sulfate-reducing and sulfur-oxidizing bacteria were also observed during the acclimation process. The aerobic acclimation process enriched a nitrifying microbial community from the landfill leachate sludge. These results suggested that the aerobic acclimation is a processing method for the nitrification ammonium oxidizing throw the enrichment of nitrifiers. Improvement of this acclimation method would allow nitrogen removal from leachate by nitrification and sulfur denitrification. Copyright © 2017 Elsevier Ltd. All rights reserved.

Meteorological factors had more impact on airborne bacterial communities than air pollutants.

PubMed

Zhen, Quan; Deng, Ye; Wang, Yaqing; Wang, Xiaoke; Zhang, Hongxing; Sun, Xu; Ouyang, Zhiyun

2017-12-01

Airborne bacteria have gained increasing attention because they affect ecological balance and pose potential risks on human health. Recently, some studies have focused on the abundance and composition of airborne bacteria under heavy, hazy polluted weather in China, but they reached different conclusions about the comparisons with non-polluted days. In this study, we tested the hypothesis that meteorological factors could have a higher impact on shaping airborne bacterial communities than air pollutants by systematically monitoring the communities for 1year. Total suspended particles in Beijing were sampled for 20 consecutive days in each season of 2015. Bacterial abundance varied from 8.71×10 3 to 2.14×10 7 ribosomal operons per cubic meter according to the quantitative PCR analysis. There were relatively higher bacterial counts in spring and in autumn than in winter and summer. Airborne bacterial communities displayed a strong seasonality, according to the hierarchical cluster analysis. Only two exceptions overtook the seasonal trend, and both occurred in or after violent meteorological changes (sandstorm or rain). Aggregated boosted tree analysis performed on bacterial abundance showed that the dominant factors shaping bacterial communities were meteorological. They were air pressure in winter, air temperature and relative humidity in spring, RH in summer, and vapor pressure in autumn. Variation partition analysis on community structure showed that meteorological factors explained more variations than air pollutants. Therefore, both of the two models verified our hypothesis that the differences in airborne bacterial communities in polluted days or non-polluted days were mainly driven by the discrepancies of meteorological factors rather than by the presence of air pollutants. Copyright © 2017 Elsevier B.V. All rights reserved.

Soil aggregate stratification of nematodes and ammonia oxidizers affects nitrification in an acid soil.

PubMed

Jiang, Yuji; Jin, Chen; Sun, Bo

2014-10-01

Nitrification plays a central role in global nitrogen cycle, which is affected by interaction between soil microfauna and microorganisms. The impact of synchronized changes in nematodes and ammonia oxidizers within aggregate fractions on nitrification was investigated in an acid soil under 10-year manure application. Nematodes, ammonia oxidizers and potential nitrification activity (PNA) were examined in three soil aggregate fractions under four fertilization regimes. Pyrosequencing data revealed that the dominant bacterial amoA operational taxonomic units (OTUs) were related to Nitrosospira species, while archaeal OTUs were affiliated with Nitrososphaera and Nitrosotalea species. PNA was more strongly correlated with ammonia-oxidizing bacteria (AOB) abundance than ammonia-oxidizing archaea (AOA) abundance, although AOA were dominant in the acid soil. Plant parasites had a negative effect on AOB abundance; however, bacterivores stimulated AOB abundance and contributed more to PNA than plant parasites. Aggregate fractions exerted significant impacts on AOA abundance and AOB community composition. Total carbon content strongly affected the abundance and composition of AOA community, while soil pH primarily affected that of AOB community. Soil variables explained 62.7% and 58.1% variations, and nematode variables explained 11.7% and 19.5% variations in the AOA and AOB community composition respectively. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Anti-Biofilm Activity of a Self-Aggregating Peptide against Streptococcus mutans

PubMed Central

Ansari, Juliana M.; Abraham, Nabil M.; Massaro, Jenna; Murphy, Kelsey; Smith-Carpenter, Jillian; Fikrig, Erol

2017-01-01

Streptococcus mutans is the primary agent of dental cavities, in large part due to its ability to adhere to teeth and create a molecular scaffold of glucan polysaccharides on the tooth surface. Disrupting the architecture of S. mutans biofilms could help undermine the establishment of biofilm communities that cause cavities and tooth decay. Here we present a synthetic peptide P1, derived from a tick antifreeze protein, which significantly reduces S. mutans biofilm formation. Incubating cells with this peptide decreased biofilm biomass by approximately 75% in both a crystal violet microplate assay and an in vitro tooth model using saliva-coated hydroxyapatite discs. Bacteria treated with peptide P1 formed irregular biofilms with disconnected aggregates of cells and exopolymeric matrix that readily detached from surfaces. Peptide P1 can bind directly to S. mutans cells but does not possess bactericidal activity. Anti-biofilm activity was correlated with peptide aggregation and β-sheet formation in solution, and alternative synthetic peptides of different lengths or charge distribution did not inhibit biofilms. This anti-biofilm peptide interferes with S. mutans biofilm formation and architecture, and may have future applications in preventing bacterial buildup on teeth. PMID:28392782

Properties of Concrete with Tire Derived Aggregate Partially Replacing Coarse Aggregates.

PubMed

Siringi, Gideon; Abolmaali, Ali; Aswath, Pranesh B

2015-01-01

Tire derived aggregate (TDA) has been proposed as a possible lightweight replacement for mineral aggregate in concrete. The role played by the amount of TDA replacing coarse aggregate as well as different treatment and additives in concrete on its properties is examined. Conventional concrete (without TDA) and concrete containing TDA are compared by examining their compressive strength based on ASTM C39, workability based on ASTM C143, splitting tensile strength based on ASTM C496, modulus of rupture (flexural strength) based on ASTM C78, and bond stress based on ASTM C234. Results indicate that while replacement of coarse aggregates with TDA results in reduction in strength, it may be mitigated with addition of silica fume to obtain the desired strength. The greatest benefit of using TDA is in the development of a higher ductile product while utilizing recycled TDA.

Protein aggregate turbidity: Simulation of turbidity profiles for mixed-aggregation reactions.

PubMed

Hall, Damien; Zhao, Ran; Dehlsen, Ian; Bloomfield, Nathaniel; Williams, Steven R; Arisaka, Fumio; Goto, Yuji; Carver, John A

2016-04-01

Due to their colloidal nature, all protein aggregates scatter light in the visible wavelength region when formed in aqueous solution. This phenomenon makes solution turbidity, a quantity proportional to the relative loss in forward intensity of scattered light, a convenient method for monitoring protein aggregation in biochemical assays. Although turbidity is often taken to be a linear descriptor of the progress of aggregation reactions, this assumption is usually made without performing the necessary checks to provide it with a firm underlying basis. In this article, we outline utilitarian methods for simulating the turbidity generated by homogeneous and mixed-protein aggregation reactions containing fibrous, amorphous, and crystalline structures. The approach is based on a combination of Rayleigh-Gans-Debye theory and approximate forms of the Mie scattering equations. Crown Copyright © 2015. Published by Elsevier Inc. All rights reserved.

Flocculation of colloidal clay by bacterial polysaccharides: effect of macromolecule charge and structure.

PubMed

Labille, J; Thomas, F; Milas, M; Vanhaverbeke, C

2005-04-01

The molecular mechanism of montmorillonite flocculation by bacterial polysaccharides was investigated, with special emphasis on the effect of carboxylic charges in the macromolecules on the mechanisms of interaction with the clay surface. An indirect way to quantify the energy of interaction was used, by comparing the flocculation ability of variously acidic polysaccharides. Data on tensile strength of aggregates in diluted suspension were collected by timed size measurements in the domain 0.1-600 microm, using laser diffraction. The flow behavior of settled aggregates was studied by rheology measurements. Flocculation of colloidal clay suspension by polysaccharides requires cancelling of the electrostatic repulsions by salts, which allows approach of clay surfaces close enough to be bridged by adsorbing macromolecules. The amount of acidic charges of the polysaccharides, and especially their location in the molecular structure, governs the bridging mechanism and the resulting tensile strength of the aggregates. The exposure of carboxylate groups located on side chains strongly promotes flocculation. In turn, charges located on the backbone of the polysaccharide are less accessible to interaction, and the flocculation ability of such polysaccharides is lowered. Measurements at different pH indicate that adsorption of acidic polysaccharides occurs via electrostatic interactions on the amphoteric edge surface of clay platelets, whereas neutral polysaccharides rather adsorb via weak interactions. Increased tensile strength in diluted aggregates due to strong surface interactions results in proportionally increased viscosity of the concentrated aggregates.

Aggregation and breakup of colloidal particle aggregates in shear flow, studied with video microscopy.

PubMed

Tolpekin, V A; Duits, M H G; van den Ende, D; Mellema, J

2004-03-30

We used video microscopy to study the behavior of aggregating suspensions in shear flow. Suspensions consisted of 920 nm diameter silica spheres, dispersed in a methanol/bromoform solvent, to which poly(ethylene glycol) (M = 35.000 g) was added to effect weak particle aggregation. With our solvent mixture, the refractive index of the particles could be closely matched, to allow microscopic observations up to 80 microm deep into the suspension. Also the mass density is nearly equal to that of the particles, thus allowing long observation times without problems due to aggregate sedimentation. Particles were visualized via fluorescent molecules incorporated into their cores. Using a fast confocal scanning laser microscope made it possible to characterize the (flowing) aggregates via their contour-area distributions as observed in the focal plane. The aggregation process was monitored from the initial state (just after adding the polymer), until a steady state was reached. The particle volume fraction was chosen at 0.001, to obtain a characteristic aggregation time of a few hundred seconds. On variation of polymer concentration, cP (2.2-12.0 g/L), and shear rate, gamma (3-6/s), it was observed that the volume-averaged size, Dv, in the steady state became larger with polymer concentration and smaller with shear rate. This demonstrates that the aggregate size is set by a competition between cohesive forces caused by the polymer and rupture forces caused by the flow. Also aggregate size distributions were be measured (semiquantitatively). Together with a description for the internal aggregate structure they allowed a modeling of the complete aggregation curve, from t = 0 up to the steady state. A satisfactory description could be obtained by describing the aggregates as fractal objects, with Df = 2.0, as measured from CSLM images after stopping the flow. In this modeling, the fitted characteristic breakup time was found to increase with cP.

Impact of wall shear stress on initial bacterial adhesion in rotating annular reactor

PubMed Central

Saur, Thibaut; Morin, Emilie; Habouzit, Frédéric; Bernet, Nicolas

2017-01-01

The objective of this study was to investigate the bacterial adhesion under different wall shear stresses in turbulent flow and using a diverse bacterial consortium. A better understanding of the mechanisms governing microbial adhesion can be useful in diverse domains such as industrial processes, medical fields or environmental biotechnologies. The impact of wall shear stress—four values ranging from 0.09 to 7.3 Pa on polypropylene (PP) and polyvinyl chloride (PVC)—was carried out in rotating annular reactors to evaluate the adhesion in terms of morphological and microbiological structures. A diverse inoculum consisting of activated sludge was used. Epifluorescence microscopy was used to quantitatively and qualitatively characterize the adhesion. Attached bacterial communities were assessed by molecular fingerprinting profiles (CE-SSCP). It has been demonstrated that wall shear stress had a strong impact on both quantitative and qualitative aspects of the bacterial adhesion. ANOVA tests also demonstrated the significant impact of wall shear stress on all three tested morphological parameters (surface coverage, number of objects and size of objects) (p-values < 2.10−16). High wall shear stresses increased the quantity of attached bacteria but also altered their spatial distribution on the substratum surface. As the shear increased, aggregates or clusters appeared and their size grew when increasing the shears. Concerning the microbiological composition, the adhered bacterial communities changed gradually with the applied shear. PMID:28207869

Actinobacillus pleuropneumoniae grows as aggregates in the lung of pigs: is it time to refine our in vitro biofilm assays?

PubMed

Tremblay, Yannick D N; Labrie, Josée; Chénier, Sonia; Jacques, Mario

2017-07-01

Actinobacillus pleuropneumoniae causes porcine pleuropneumonia and forms biofilms in vitro on abiotic surfaces; however, presence of biofilms during infections has not been documented. The aim of this study was to use a species-specific fluorescent oligonucleotide probe and confocal microscopy to localize A. pleuropneumoniae in the lungs of two naturally infected pigs. Actinobacillus pleuropneumoniae was detected by fluorescence in situ hybridization and observed to grow as aggregates (~30-45 μm) during a natural infection. As the A. pleuropneumoniae aggregates observed in porcine lungs differed from the biofilms grown on a solid surface obtained in vitro, we designed a new biofilm assay using agarose, a porous substrate, favouring the formation of aggregates. In this study, we described for the first time the mode of growth of A. pleuropneumoniae during a natural infection in pigs. We also propose an in vitro biofilm assay for A. pleuropneumoniae using a porous substrate which allows the formation of aggregates. This assay might be more representative of the in vivo situation, at least in terms of the size of the bacterial aggregates and the presence of a porous matrix, and could potentially be used to test the susceptibility of A. pleuropneumoniae aggregates to antibiotics and disinfectants. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Organic carbon, water repellency and soil stability to slaking at aggregate and intra-aggregate scales

NASA Astrophysics Data System (ADS)

Jordán López, Antonio; García-Moreno, Jorge; Gordillo-Rivero, Ángel J.; Zavala, Lorena M.; Cerdà, Artemi; Alanís, Nancy; Jiménez-Compán, Elizabeth

2015-04-01

Water repellency (WR) is a property of some soils that inhibits or delays water infiltration between a few seconds and days or weeks. Inhibited or delayed infiltration contributes to ponding and increases runoff flow generation, often increasing soil erosion risk. In water-repellent soils, water infiltrates preferentially through cracks or macropores, causing irregular soil wetting patterns, the development of preferential flow paths and accelerated leaching of nutrients. Although low inputs of hydrophobic organic substances and high mineralization rates lead to low degrees of WR in cropped soils, it has been reported that conservative agricultural practices may induce soil WR. Although there are many studies at catchment, slope or plot scales very few studies have been carried out at particle or aggregate scale. Intra-aggregate heterogeneity of physical, biological and chemical properties conditions the transport of substances, microbial activity and biochemical processes, including changes in the amount, distribution and chemical properties of organic matter. Some authors have reported positive relationships between soil WR and aggregate stability, since it may delay the entry of water into aggregates, increase structural stability and contribute to reduce soil erosion risk. Organic C (OC) content, aggregate stability and WR are therefore strongly related parameters. In the case of agricultural soils, where both the type of management as crops can influence all these parameters, it is important to evaluate the interactions among them and their consequences. Studies focused on the intra-aggregate distribution of OC and WR are necessary to shed light on the soil processes at a detailed scale. It is extremely important to understand how the spatial distribution of OC in soil aggregates can protect against rapid water entry and help stabilize larger structural units or lead to preferential flow. The objectives of this research are to study [i] the OC content and the

Properties of Concrete with Tire Derived Aggregate Partially Replacing Coarse Aggregates

PubMed Central

Siringi, Gideon; Abolmaali, Ali; Aswath, Pranesh B.

2015-01-01

Tire derived aggregate (TDA) has been proposed as a possible lightweight replacement for mineral aggregate in concrete. The role played by the amount of TDA replacing coarse aggregate as well as different treatment and additives in concrete on its properties is examined. Conventional concrete (without TDA) and concrete containing TDA are compared by examining their compressive strength based on ASTM C39, workability based on ASTM C143, splitting tensile strength based on ASTM C496, modulus of rupture (flexural strength) based on ASTM C78, and bond stress based on ASTM C234. Results indicate that while replacement of coarse aggregates with TDA results in reduction in strength, it may be mitigated with addition of silica fume to obtain the desired strength. The greatest benefit of using TDA is in the development of a higher ductile product while utilizing recycled TDA. PMID:26161440

Methods of predicting aggregate voids.

DOT National Transportation Integrated Search

2013-03-01

Percent voids in combined aggregates vary significantly. Simplified methods of predicting aggregate : voids were studied to determine the feasibility of a range of gradations using aggregates available in Kansas. : The 0.45 Power Curve Void Predictio...

Blended aggregate study : final report.

DOT National Transportation Integrated Search

1980-03-01

Louisiana produces no naturally occurring skid resistant aggregate and, therefore, must import these aggregates at great expense. : In an effort to extend the yield of these aggregates, a laboratory investigation was initiated to determine the feasib...

Soil aggregation and aggregate-associated carbon under four typical halophyte communities in an arid area.

PubMed

Yang, Haichang; Wang, Jingya; Zhang, Fenghua

2016-12-01

The soil microbial biomass carbon (MBC) is considered as a sensitive index of soil carbon ecosystem. The distribution of aggregate-associated MBC determines the capacity of the soil to store soil organic carbon (SOC). We compared soil aggregate-associated SOC and aggregate-associated MBC under four halophyte communities: Karelinia caspia (Pall.) Less. (Abbr. K. caspia), Bassia dasyphylla (Fisch. et C. A. Mey.) Kuntze. (Abbr. B. dasyphylla), Haloxylon ammodendron (C. A. Mey.) Bunge. (Abbr. H. ammodendron), and Tamarix ramosissima Lour (Abbr. T. ramosissima) on an alluvial fan in the Manasi River Basin, Xinjiang, China. The specific objectives of the study were to determine which aggregate size fraction was the most important for MBC and SOC retention in these soils of four halophyte communities. The results showed that the 0.053-0.25 mm fraction contained 47 to 75 % of the total soil mass. The amount of soil in the 0.053-0.25 mm fraction was significantly greater than that in the >0.25 and the <0.053 mm fractions. The >0.25 and the <0.053 mm fractions contained 7.8 to 43.0 % of the soil mass. Aggregate-associated SOC concentrations ranged from 1.70 to 13.68 g kg -1 , and the aggregate-associated SOC were the highest under the H. ammodendron and T. ramosissima communities. The aggregate-associated MBC ranged from 55.26 to 217.11 g kg -1 , and the aggregate-associated MBC were higher under the K. caspia and B. dasyphylla communities. The aggregate-associated SOC concentrations were significantly higher in the >0.25 and the <0.053 mm fractions than in the 0.053-0.25 mm fraction. The aggregate-associated MBC in the 20-40 cm depth was consistent with its law. However, in the 0-20 cm depth, the aggregate-associated MBC concentrations were significantly higher in the >0.25 mm fraction than the other two aggregate fractions, and there were no significant differences in 0.25-0.053 or <0.053 mm fraction. Correlation analyses showed that the aggregate

Layer-by-layer carbon nanotube bio-templates for in situ monitoring of the metabolic activity of nitrifying bacteria

NASA Astrophysics Data System (ADS)

Loh, Kenneth J.; Guest, Jeremy S.; Ho, Genevieve; Lynch, Jerome P.; Love, Nancy G.

2009-03-01

Despite the wide variety of effective disinfection and wastewater treatment techniques for removing organic and inorganic wastes, pollutants such as nitrogen remain in wastewater effluents. If left untreated, these nitrogenous wastes can adversely impact the environment by promoting the overgrowth of aquatic plants, depleting dissolved oxygen, and causing eutrophication. Although nitrification/denitrification processes are employed during advanced wastewater treatment, effective and efficient operation of these facilities require information of the pH, dissolved oxygen content, among many other parameters, of the wastewater effluent. In this preliminary study, a biocompatible CNT-based nanocomposite is proposed and validated for monitoring the biological metabolic activity of nitrifying bacteria in wastewater effluent environments (i.e., to monitor the nitrification process). Using carbon nanotubes and a pH-sensitive conductive polymer (i.e., poly(aniline) emeraldine base), a layer-by-layer fabrication technique is employed to fabricate a novel thin film pH sensor that changes its electrical properties in response to variations in ambient pH environments. Laboratory studies are conducted to evaluate the proposed nanocomposite's biocompatibility with wastewater effluent environments and its pH sensing performance.

Nitrifying aerobic granular sludge fermentation for releases of carbon source and phosphorus: The role of fermentation pH.

PubMed

Zou, Jinte; Pan, Jiyang; He, Hangtian; Wu, Shuyun; Xiao, Naidong; Ni, Yongjiong; Li, Jun

2018-07-01

The effect of fermentation pH (uncontrolled, 4 and 10) on the releases of carbon source and phosphorus from nitrifying aerobic granular sludge (N-AGS) was investigated. Meanwhile, metal ion concentration and microbial community characterization were explored during N-AGS fermentation. The results indicated that N-AGS fermentation at pH 10 significantly promoted the releases of soluble chemical oxygen demand (SCOD) and total volatile fatty acids (TVFAs). However, SCOD and TVFA released from N-AGS were inhibited at pH 4. Moreover, acidic condition promoted phosphorus release (mainly apatite) from N-AGS during anaerobic fermentation. Nevertheless, alkaline condition failed to increase phosphorus concentration due to the formation of chemical-phosphate precipitates. Compared with the previously reported flocculent sludge fermentation, N-AGS fermentation released more SCOD and TVFAs, possibly due to the greater extracellular polymeric substances content and some hydrolytic-acidogenic bacteria in N-AGS. Therefore, N-AGS alkaline fermentation facilitated the carbon source recovery, while N-AGS acidic fermentation benefited the phosphorus recovery. Copyright © 2018. Published by Elsevier Ltd.

Kinetics of Aggregation with Choice

DOE PAGES

Ben-Naim, Eli; Krapivsky, Paul

2016-12-01

Here we generalize the ordinary aggregation process to allow for choice. In ordinary aggregation, two random clusters merge and form a larger aggregate. In our implementation of choice, a target cluster and two candidate clusters are randomly selected and the target cluster merges with the larger of the two candidate clusters.We study the long-time asymptotic behavior and find that as in ordinary aggregation, the size density adheres to the standard scaling form. However, aggregation with choice exhibits a number of different features. First, the density of the smallest clusters exhibits anomalous scaling. Second, both the small-size and the large-size tailsmore » of the density are overpopulated, at the expense of the density of moderate-size clusters. Finally, we also study the complementary case where the smaller candidate cluster participates in the aggregation process and find an abundance of moderate clusters at the expense of small and large clusters. Additionally, we investigate aggregation processes with choice among multiple candidate clusters and a symmetric implementation where the choice is between two pairs of clusters.« less

Soil aggregation and aggregating agents as affected by long term contrasting management of an Anthrosol

NASA Astrophysics Data System (ADS)

Zhang, Shulan; Wang, Renjie; Yang, Xueyun; Sun, Benhua; Li, Qinghui

2016-12-01

Soil aggregation was studied in a 21-year experiment conducted on an Anthrosol. The soil management regimes consisted of cropland abandonment, bare fallow without vegetation and cropping system. The cropping system was combined with the following nutrient management treatments: control (CONTROL, no nutrient input); nitrogen, phosphorus and potassium (NPK); straw plus NPK (SNPK); and manure (M) plus NPK (MNPK). Compared with the CONTROL treatment, the abandonment treatment significantly increased the formation of large soil macroaggregates (>2 mm) and consequently improved the stability of aggregates in the surface soil layer due to enhancement of hyphal length and of soil organic matter content. However, in response to long-term bare fallow treatment aggregate stability was low, as were the levels of aggregating agents. Long term fertilization significantly redistributed macroaggregates; this could be mainly ascribed to soil organic matter contributing to the formation of 0.5-2 mm classes of aggregates and a decrease in the formation of the >2 mm class of aggregates, especially in the MNPK treatment. Overall, hyphae represented a major aggregating agent in both of the systems tested, while soil organic compounds played significantly different roles in stabilizing aggregates in Anthrosol when the cropping system and the soil management regimes were compared.

Soil aggregation and aggregating agents as affected by long term contrasting management of an Anthrosol

PubMed Central

Zhang, Shulan; Wang, Renjie; Yang, Xueyun; Sun, Benhua; Li, Qinghui

2016-01-01

Soil aggregation was studied in a 21-year experiment conducted on an Anthrosol. The soil management regimes consisted of cropland abandonment, bare fallow without vegetation and cropping system. The cropping system was combined with the following nutrient management treatments: control (CONTROL, no nutrient input); nitrogen, phosphorus and potassium (NPK); straw plus NPK (SNPK); and manure (M) plus NPK (MNPK). Compared with the CONTROL treatment, the abandonment treatment significantly increased the formation of large soil macroaggregates (>2 mm) and consequently improved the stability of aggregates in the surface soil layer due to enhancement of hyphal length and of soil organic matter content. However, in response to long-term bare fallow treatment aggregate stability was low, as were the levels of aggregating agents. Long term fertilization significantly redistributed macroaggregates; this could be mainly ascribed to soil organic matter contributing to the formation of 0.5–2 mm classes of aggregates and a decrease in the formation of the >2 mm class of aggregates, especially in the MNPK treatment. Overall, hyphae represented a major aggregating agent in both of the systems tested, while soil organic compounds played significantly different roles in stabilizing aggregates in Anthrosol when the cropping system and the soil management regimes were compared. PMID:27958366

Bacterial community transcription patterns during a marine phytoplankton bloom.

PubMed

Rinta-Kanto, Johanna M; Sun, Shulei; Sharma, Shalabh; Kiene, Ronald P; Moran, Mary Ann

2012-01-01

Bacterioplankton consume a large proportion of photosynthetically fixed carbon in the ocean and control its biogeochemical fate. We used an experimental metatranscriptomics approach to compare bacterial activities that route energy and nutrients during a phytoplankton bloom compared with non-bloom conditions. mRNAs were sequenced from duplicate bloom and control microcosms 1 day after a phytoplankton biomass peak, and transcript copies per litre of seawater were calculated using an internal mRNA standard. Transcriptome analysis revealed a potential novel mechanism for enhanced efficiency during carbon-limited growth, mediated through membrane-bound pyrophosphatases [V-type H(+)-translocating; hppA]; bloom bacterioplankton participated less in this metabolic energy scavenging than non-bloom bacterioplankton, with possible implications for differences in growth yields on organic substrates. Bloom bacterioplankton transcribed more copies of genes predicted to increase cell surface adhesiveness, mediated by changes in bacterial signalling molecules related to biofilm formation and motility; these may be important in microbial aggregate formation. Bloom bacterioplankton also transcribed more copies of genes for organic acid utilization, suggesting an increased importance of this compound class in the bioreactive organic matter released during phytoplankton blooms. Transcription patterns were surprisingly faithful within a taxon regardless of treatment, suggesting that phylogeny broadly predicts the ecological roles of bacterial groups across 'boom' and 'bust' environmental backgrounds. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

A study of the aggregation of cyclodextrins: Determination of the critical aggregation concentration, size of aggregates and thermodynamics using isodesmic and K2-K models.

PubMed

Do, Thao Thi; Van Hooghten, Rob; Van den Mooter, Guy

2017-04-15

The aggregation of three different cyclodextrins (CDs): 2-hydroxypropyl-β-cyclodextrin (HP-β-CD), 2-hydroxypropyl-γ-cyclodextrin (HP-γ-CD) and sulfobutylether-β-cyclodextrin (SBE-β-CD) was studied. The critical aggregation concentration (cac) of these three CDs is quite similar and is situated at ca. 2% (m/v). There was only a small difference in the cac values determined by DLS and 1 H NMR. DLS measurements revealed that CDs in solution have three size populations wherein one of them is that of a single CD molecule. The size of aggregates determined by TEM appears to be similar to the size of the aggregates in the second size distribution determined by DLS. Isodesmic and K 2 -K self-assembly models were used for studying the aggregation process of HP-β-CD, HP-γ-CD and SBE-β-CD. The results showed that the aggregation process of these CDs is a cooperative one, where the first step of aggregation is less favorable than the next steps. The determined thermodynamic parameters showed that the aggregation process of all three CDs is spontaneous and exothermic and it is driven by an increase of the entropy of the environment. Copyright © 2017 Elsevier B.V. All rights reserved.

Antibody blocks acquisition of bacterial colonization through agglutination

PubMed Central

Roche, A. M.; Richard, A. L.; Rahkola, J. T.; Janoff, E. N.; Weiser, J. N.

2014-01-01

Invasive infection often begins with asymptomatic colonization of mucosal surfaces. A murine model of bacterial colonization with Streptococcus pneumoniae was used to study the mechanism for mucosal protection by immunoglobulin. In previously colonized immune mice, bacteria were rapidly sequestered within large aggregates in the nasal lumen. To further examine the role of bacterial agglutination in protection by specific antibodies, mice were passively immunized with IgG purified from anti-pneumococcal sera or pneumococcal type-specific monoclonal human IgA (hIgA1 or hIgA2). Systemically-delivered IgG accessed the mucosal surface and blocked acquisition of colonization and transmission between littermates. Optimal protection by IgG was independent of Fc fragment and complement and, therefore, did not involve an opsonophagocytic mechanism. Enzymatic digestion or reduction of IgG prior to administration showed that protection required divalent binding that maintained its agglutinating effect. Divalent hIgA1 is cleaved by the pneumococcal member of a family of bacterial proteases that generate monovalent Fabα fragments. Thus, passive immunization with hIgA1 blocked colonization by an IgA1-protease deficient mutant (agglutinated), but not the protease-producing wild-type parent (not agglutinated), whereas protease-resistant hIgA2 agglutinated and blocked colonization by both. Our findings highlight the importance of agglutinating antibodies in mucosal defense and reveal how successful pathogens evade this effect. PMID:24962092

[Species diversity and ecological distribution of anaerobic ammonium-oxidizing bacteria].

PubMed

Chen, Ting-Ting; Zheng, Ping; Hu, Bao-Lan

2009-05-01

Anaerobic ammonium oxidation (anammox) is an important discovery in microbiology and environmental sciences, which can simultaneously remove NH4(+) -N and NO3(-) -N, being valuable in environmental engineering. However, anaerobic ammonium oxidizers are extremely slow-growing, and their population's doubling time is longer than 11 days, which seriously restricts the application of anammox process. Therefore, the study of anammox bacteria is of significance. It has been proved that besides planctomycetes, the first recognized anammox bacteria, both nitrifying bacteria and denitrifying bacteria are also capable of anaerobic ammonium oxidation. These anammox bacteria have wide-spread habitats, which offered a chance to exploit new bacterial resources for anammox. Nitrifying bacteria and denitrifying bacteria have the function of anammox, and their metabolic diversity provides a basis to speed up the start-up of anammox reactor. It was revealed that anaerobic digestion sludge can present anammox activity, with sulphate as electron acceptor. The new bioreaction lays a foundation for the development of novel N-removal biotechnology, being conducive to the development and application of anammox to get more bacterial resources for anammox and to make clear the ecological distribution of anammox bacteria.

Lithologic characterization of active ITD aggregate sources and implications for aggregate quality.

DOT National Transportation Integrated Search

2014-03-01

Aggregate from 40 material sources across Idaho were sampled and the lithologies identified quantitatively. Aggregate compositions are compared with commercial AASHTO T 303 and ASTM C1293 results and the geologic map of Idaho to identify those rock t...

Aggregation and disaggregation kinetics of human blood platelets: Part II. Shear-induced platelet aggregation.

PubMed Central

Huang, P Y; Hellums, J D

1993-01-01

A population balance equation (PBE) mathematical model for analyzing platelet aggregation kinetics was developed in Part I (Huang, P. Y., and J. D. Hellums. 1993. Biophys. J. 65: 334-343) of a set of three papers. In this paper, Part II, platelet aggregation and related reactions are studied in the uniform, known shear stress field of a rotational viscometer, and interpreted by means of the model. Experimental determinations are made of the platelet-aggregate particle size distributions as they evolve in time under the aggregating influence of shear stress. The PBE model is shown to give good agreement with experimental determinations when either a reversible (aggregation and disaggregation) or an irreversible (no disaggregation) form of the model is used. This finding suggests that for the experimental conditions studied disaggregation processes are of only secondary importance. During shear-induced platelet aggregation, only a small fraction of platelet collisions result in the binding together of the involved platelets. The modified collision efficiency is approximately zero for shear rates below 3000 s-1. It increases with shear rates above 3000 s-1 to about 0.01 for a shear rate of 8000 s-1. Addition of platelet chemical agonists yields order of magnitude increases in collision efficiency. The collision efficiency for shear-induced platelet aggregation is about an order of magnitude less at 37 degrees C than at 24 degrees C. The PBE model gives a much more accurate representation of aggregation kinetics than an earlier model based on a monodispersed particle size distribution. PMID:8369442

Model for amorphous aggregation processes

NASA Astrophysics Data System (ADS)

Stranks, Samuel D.; Ecroyd, Heath; van Sluyter, Steven; Waters, Elizabeth J.; Carver, John A.; von Smekal, Lorenz

2009-11-01

The amorphous aggregation of proteins is associated with many phenomena, ranging from the formation of protein wine haze to the development of cataract in the eye lens and the precipitation of recombinant proteins during their expression and purification. While much literature exists describing models for linear protein aggregation, such as amyloid fibril formation, there are few reports of models which address amorphous aggregation. Here, we propose a model to describe the amorphous aggregation of proteins which is also more widely applicable to other situations where a similar process occurs, such as in the formation of colloids and nanoclusters. As first applications of the model, we have tested it against experimental turbidimetry data of three proteins relevant to the wine industry and biochemistry, namely, thaumatin, a thaumatinlike protein, and α -lactalbumin. The model is very robust and describes amorphous experimental data to a high degree of accuracy. Details about the aggregation process, such as shape parameters of the aggregates and rate constants, can also be extracted.

Heating of Porous Icy Dust Aggregates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sirono, Sin-iti

At the beginning of planetary formation, highly porous dust aggregates are formed through coagulation of dust grains. Outside the snowline, the main component of an aggregate is H{sub 2}O ice. Because H{sub 2}O ice is formed in amorphous form, its thermal conductivity is extremely small. Therefore, the thermal conductivity of an icy dust aggregate is low. There is a possibility of heating inside an aggregate owing to the decay of radionuclides. It is shown that the temperature increases substantially inside an aggregate, leading to crystallization of amorphous ice. During the crystallization, the temperature further increases sufficiently to continue sintering. Themore » mechanical properties of icy dust aggregates change, and the collisional evolution of dust aggregates is affected by the sintering.« less

Water relations in the interaction of foliar bacterial pathogens with plants.

PubMed

Beattie, Gwyn A

2011-01-01

This review examines the many ways in which water influences the relations between foliar bacterial pathogens and plants. As a limited resource in aerial plant tissues, water is subject to manipulation by both plants and pathogens. A model is emerging that suggests that plants actively promote localized desiccation at the infection site and thus restrict pathogen growth as one component of defense. Similarly, many foliar pathogens manipulate water relations as one component of pathogenesis. Nonvascular pathogens do this using effectors and other molecules to alter hormonal responses and enhance intercellular watersoaking, whereas vascular pathogens use many mechanisms to cause wilt. Because of water limitations on phyllosphere surfaces, bacterial colonists, including pathogens, benefit from the protective effects of cellular aggregation, synthesis of hygroscopic polymers, and uptake and production of osmoprotective compounds. Moreover, these bacteria employ tactics for scavenging and distributing water to overcome water-driven barriers to nutrient acquisition, movement, and signal exchange on plant surfaces. Copyright © 2011 by Annual Reviews. All rights reserved.

Elucidating the impact of micro-scale heterogeneous bacterial distribution on biodegradation

NASA Astrophysics Data System (ADS)

Schmidt, Susanne I.; Kreft, Jan-Ulrich; Mackay, Rae; Picioreanu, Cristian; Thullner, Martin

2018-06-01

Groundwater microorganisms hardly ever cover the solid matrix uniformly-instead they form micro-scale colonies. To which extent such colony formation limits the bioavailability and biodegradation of a substrate is poorly understood. We used a high-resolution numerical model of a single pore channel inhabited by bacterial colonies to simulate the transport and biodegradation of organic substrates. These high-resolution 2D simulation results were compared to 1D simulations that were based on effective rate laws for bioavailability-limited biodegradation. We (i) quantified the observed bioavailability limitations and (ii) evaluated the applicability of previously established effective rate concepts if microorganisms are heterogeneously distributed. Effective bioavailability reductions of up to more than one order of magnitude were observed, showing that the micro-scale aggregation of bacterial cells into colonies can severely restrict the bioavailability of a substrate and reduce in situ degradation rates. Effective rate laws proved applicable for upscaling when using the introduced effective colony sizes.

Fractal aggregates in tennis ball systems

NASA Astrophysics Data System (ADS)

Sabin, J.; Bandín, M.; Prieto, G.; Sarmiento, F.

2009-09-01

We present a new practical exercise to explain the mechanisms of aggregation of some colloids which are otherwise not easy to understand. We have used tennis balls to simulate, in a visual way, the aggregation of colloids under reaction-limited colloid aggregation (RLCA) and diffusion-limited colloid aggregation (DLCA) regimes. We have used the images of the cluster of balls, following Forrest and Witten's pioneering studies on the aggregation of smoke particles, to estimate their fractal dimension.

Protein aggregation and prionopathies.

PubMed

Renner, M; Melki, R

2014-06-01

Prion protein and prion-like proteins share a number of characteristics. From the molecular point of view, they are constitutive proteins that aggregate following conformational changes into insoluble particles. These particles escape the cellular clearance machinery and amplify by recruiting the soluble for of their constituting proteins. The resulting protein aggregates are responsible for a number of neurodegenerative diseases such as Creutzfeldt-Jacob, Alzheimer, Parkinson and Huntington diseases. In addition, there are increasing evidences supporting the inter-cellular trafficking of these aggregates, meaning that they are "transmissible" between cells. There are also evidences that brain homogenates from individuals developing Alzheimer and Parkinson diseases propagate the disease in recipient model animals in a manner similar to brain extracts of patients developing Creutzfeldt-Jacob's disease. Thus, the propagation of protein aggregates from cell to cell may be a generic phenomenon that contributes to the evolution of neurodegenerative diseases, which has important consequences on human health issues. Moreover, although the distribution of protein aggregates is characteristic for each disease, new evidences indicate the possibility of overlaps and crosstalk between the different disorders. Despite the increasing evidences that support prion or prion-like propagation of protein aggregates, there are many unanswered questions regarding the mechanisms of toxicity and this is a field of intensive research nowadays. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Role of streams in myxobacteria aggregate formation

NASA Astrophysics Data System (ADS)

Kiskowski, Maria A.; Jiang, Yi; Alber, Mark S.

2004-10-01

Cell contact, movement and directionality are important factors in biological development (morphogenesis), and myxobacteria are a model system for studying cell-cell interaction and cell organization preceding differentiation. When starved, thousands of myxobacteria cells align, stream and form aggregates which later develop into round, non-motile spores. Canonically, cell aggregation has been attributed to attractive chemotaxis, a long range interaction, but there is growing evidence that myxobacteria organization depends on contact-mediated cell-cell communication. We present a discrete stochastic model based on contact-mediated signaling that suggests an explanation for the initialization of early aggregates, aggregation dynamics and final aggregate distribution. Our model qualitatively reproduces the unique structures of myxobacteria aggregates and detailed stages which occur during myxobacteria aggregation: first, aggregates initialize in random positions and cells join aggregates by random walk; second, cells redistribute by moving within transient streams connecting aggregates. Streams play a critical role in final aggregate size distribution by redistributing cells among fewer, larger aggregates. The mechanism by which streams redistribute cells depends on aggregate sizes and is enhanced by noise. Our model predicts that with increased internal noise, more streams would form and streams would last longer. Simulation results suggest a series of new experiments.

Aggregate breakdown of nanoparticulate titania

NASA Astrophysics Data System (ADS)

Venugopal, Navin

Six nanosized titanium dioxide powders synthesized from a sulfate process were investigated. The targeted end-use of this powder was for a de-NOx catalyst honeycomb monolith. Alteration of synthesis parameters had resulted principally in differences in soluble ion level and specific surface area of the powders. The goal of this investigation was to understand the role of synthesis parameters in the aggregation behavior of these powders. Investigation via scanning electron microscopy of the powders revealed three different aggregation iterations at specific length scales. Secondary and higher order aggregate strength was investigated via oscillatory stress rheometry as a means of simulating shear conditions encountered during extrusion. G' and G'' were measured as a function of the applied oscillatory stress. Oscillatory rheometry indicated a strong variation as a function of the sulfate level of the particles in the viscoelastic yield strengths. Powder yield stresses ranged from 3.0 Pa to 24.0 Pa of oscillatory stress. Compaction curves to 750 MPa found strong similarities in extrapolated yield point of stage I and II compaction for each of the powders (at approximately 500 MPa) suggesting that the variation in sulfate was greatest above the primary aggregate level. Scanning electron microscopy of samples at different states of shear in oscillatory rheometry confirmed the variation in the linear elastic region and the viscous flow regime. A technique of this investigation was to approach aggregation via a novel perspective: aggregates are distinguished as being loose open structures that are highly disordered and stochastic in nature. The methodology used was to investigate the shear stresses required to rupture the various aggregation stages encountered and investigate the attempt to realign the now free-flowing constituents comprising the aggregate into a denser configuration. Mercury porosimetry was utilized to measure the pore size of the compact resulting from

Spatial and temporal features of the growth of a bacterial species colonizing the zebrafish gut.

PubMed

Jemielita, Matthew; Taormina, Michael J; Burns, Adam R; Hampton, Jennifer S; Rolig, Annah S; Guillemin, Karen; Parthasarathy, Raghuveer

2014-12-16

The vertebrate intestine is home to microbial ecosystems that play key roles in host development and health. Little is known about the spatial and temporal dynamics of these microbial communities, limiting our understanding of fundamental properties, such as their mechanisms of growth, propagation, and persistence. To address this, we inoculated initially germ-free zebrafish larvae with fluorescently labeled strains of an Aeromonas species, representing an abundant genus in the zebrafish gut. Using light sheet fluorescence microscopy to obtain three-dimensional images spanning the gut, we quantified the entire bacterial load, as founding populations grew from tens to tens of thousands of cells over several hours. The data yield the first ever measurements of the growth kinetics of a microbial species inside a live vertebrate intestine and show dynamics that robustly fit a logistic growth model. Intriguingly, bacteria were nonuniformly distributed throughout the gut, and bacterial aggregates showed considerably higher growth rates than did discrete individuals. The form of aggregate growth indicates intrinsically higher division rates for clustered bacteria, rather than surface-mediated agglomeration onto clusters. Thus, the spatial organization of gut bacteria both relative to the host and to each other impacts overall growth kinetics, suggesting that spatial characterizations will be an important input to predictive models of host-associated microbial community assembly. Our intestines are home to vast numbers of microbes that influence many aspects of health and disease. Though we now know a great deal about the constituents of the gut microbiota, we understand very little about their spatial structure and temporal dynamics in humans or in any animal: how microbial populations establish themselves, grow, fluctuate, and persist. To address this, we made use of a model organism, the zebrafish, and a new optical imaging technique, light sheet fluorescence microscopy

GENERAL: Kinetic Behaviors of Catalysis-Driven Growth of Three-Species Aggregates on Base of Exchange-Driven Aggregations

NASA Astrophysics Data System (ADS)

Sun, Yun-Fei; Chen, Dan; Lin, Zhen-Quan; Ke, Jian-Hong

2009-06-01

We propose a solvable aggregation model to mimic the evolution of population A, asset B, and the quantifiable resource C in a society. In this system, the population and asset aggregates themselves grow through self-exchanges with the rate kernels K1(k, j) = K1kj and K2(k, j) = K2kj, respectively. The actions of the population and asset aggregations on the aggregation evolution of resource aggregates are described by the population-catalyzed monomer death of resource aggregates and asset-catalyzed monomer birth of resource aggregates with the rate kernels J1(k, j) = J1k and J2(k, j) = J2k, respectively. Meanwhile, the asset and resource aggregates conjunctly catalyze the monomer birth of population aggregates with the rate kernel I1(k, i, j) = I1kiμjη, and population and resource aggregates conjunctly catalyze the monomer birth of asset aggregates with the rate kernel I2(k, i, j) = I2kivjη. The kinetic behaviors of species A, B, and C are investigated by means of the mean-field rate equation approach. The effects of the population-catalyzed death and asset-catalyzed birth on the evolution of resource aggregates based on the self-exchanges of population and asset appear in effective forms. The coefficients of the effective population-catalyzed death and the asset-catalyzed birth are expressed as J1e = J1/K1 and J2e = J2/K2, respectively. The aggregate size distribution of C species is found to be crucially dominated by the competition between the effective death and the effective birth. It satisfies the conventional scaling form, generalized scaling form, and modified scaling form in the cases of J1e < J2e, J1e = J2e, and J1e > J2e, respectively. Meanwhile, we also find the aggregate size distributions of populations and assets both fall into two distinct categories for different parameters μ, ν, and η: (i) When μ = ν = η = 0 and μ = ν = 0, η = 1, the population and asset aggregates obey the generalized scaling forms; and (ii) When μ = ν = 1, η = 0

Fractal Aggregates in Tennis Ball Systems

ERIC Educational Resources Information Center

Sabin, J.; Bandin, M.; Prieto, G.; Sarmiento, F.

2009-01-01

We present a new practical exercise to explain the mechanisms of aggregation of some colloids which are otherwise not easy to understand. We have used tennis balls to simulate, in a visual way, the aggregation of colloids under reaction-limited colloid aggregation (RLCA) and diffusion-limited colloid aggregation (DLCA) regimes. We have used the…

Particle-associated extracellular enzyme activity and bacterial community composition across the Canadian Arctic Ocean.

PubMed

Kellogg, Colleen T E; Deming, Jody W

2014-08-01

Microbial enzymatic hydrolysis of marine-derived particulate organic carbon (POC) can be a dominant mechanism for attenuating carbon flux in cold Arctic waters during spring and summer. Whether this mechanism depends on composition of associated microbial communities and extends into other seasons is not known. Bacterial community composition (BCC) and extracellular enzyme activity (EEA, for leucine aminopeptidases, glucosidases and chitobiases) were measured on small suspended particles and potentially sinking aggregates collected during fall from waters of the biologically productive North Water and river-impacted Beaufort Sea. Although other environmental variables appeared influential, both BCC and EEA varied along a marine productivity gradient in the two regions. Aggregates harbored the most distinctive bacterial communities, with a small number of taxa driving differences between particle-size classes (1.0-60 and > 60 μm) and free-living bacteria (0.2-1.0 μm). Significant relationships between patterns in particle-associated BCC and EEA suggest strong links between these two variables. Calculations indicated that up to 80% of POC in the euphotic zone of the North Water, and 20% in the Beaufort Sea, may be hydrolyzed enzymatically, underscoring the importance of this mechanism in attenuating carbon fluxes in Arctic waters even as winter approaches. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Characterization of bacterial functional groups and microbial activity in microcosms with glyphosate application

NASA Astrophysics Data System (ADS)

Moyano, Sofia; Bonetto, Mariana; Baigorria, Tomas; Pegoraro, Vanesa; Ortiz, Jimena; Faggioli, Valeria; Conde, Belen; Cazorla, Cristian; Boccolini, Monica

2017-04-01

Glyphosate is a worldwide used herbicide as c. 90% of transgenic crops are tolerant to it. Microbial degradation of glyphosate molecule in soil is considered the most important process that determines its persistence in the environment. However, the impact of this herbicide on target groups of soil biota remains poorly understood. Our objective was to characterize the abundance of bacterial groups and global microbial activity, under controlled conditions with application of increasing doses of glyphosate. A bioassay was carried out in microcosms using an agricultural soil (Typic Argiudoll) with registered history of glyphosate application from National Institute of Agricultural Technology (INTA, EEA Marcos Juarez, Argentina). Glyphosate of commercial formulation (74.7%) was used and the following treatments were evaluated: Soil without glyphosate (control), and Soil with doses equivalent to 1.12 and 11.2 kg ai ha-1. Microbiological parameters were estimated at 3, 7, 14 and 21 days after herbicide application by counting heterotrophic, cellulolytic, nitrogen fixing (N), and nitrifying bacteria; and fluorescein diacetate hydrolysis (FDA), microbial respiration (MR) and microbial biomass (C-BM). The N cycle related bacteria showed greater sensitivity to glyphosate with significant increases in abundance. On the other hand the C cycle parameters were strongly conditioned by the time elapsed since the application of the herbicide, as did the MR. The FDA declined with the highest dose, while the C-BM was not affected. Therefore, we conclude that in the studied experimental conditions glyphosate stimulated bacterial growth (i.e. target abundances) representing a source of N, C and nutrients. On the other hand, enzymatic activity (FDA) decreased when glyphosate was applied in the highest dose, whereas, it had no effect on the MR nor C-BM, which could be attributable to the organic matter content of the soil. However, future research in field conditions is necessary, for

A comparative study on the aggregating effects of guanidine thiocyanate, guanidine hydrochloride and urea on lysozyme aggregation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Emadi, Saeed, E-mail: emadi@iasbs.ac.ir; Behzadi, Maliheh

Highlights: • Lysozyme aggregated in guanidine thiocyanate (1.0 and 2.0 M). • Lysozyme aggregated in guanidine hydrochloride (4 and 5 M). • Lysozyme did not aggregated at any concentration (0.5–5 M) of urea. • Unfolding pathway is more important than unfolding per se in aggregation. - Abstract: Protein aggregation and its subsequent deposition in different tissues culminate in a diverse range of diseases collectively known as amyloidoses. Aggregation of hen or human lysozyme depends on certain conditions, namely acidic pH or the presence of additives. In the present study, the effects on the aggregation of hen egg-white lysozyme via incubationmore » in concentrated solutions of three different chaotropic agents namely guanidine thiocyanate, guanidine hydrochloride and urea were investigated. Here we used three different methods for the detection of the aggregates, thioflavin T fluorescence, circular dichroism spectroscopy and atomic force microscopy. Our results showed that upon incubation with different concentrations (0.5, 1.0, 2.0, 3.0, 4.0, 5.0 M) of the chemical denaturants, lysozyme was aggregated at low concentrations of guanidine thiocyanate (1.0 and 2.0 M) and at high concentrations of guanidine hydrochloride (4 and 5 M), although no fibril formation was detected. In the case of urea, no aggregation was observed at any concentration.« less

Molecular aggregation of humic substances

USGS Publications Warehouse

Wershaw, R. L.

1999-01-01

Humic substances (HS) form molecular aggregates in solution and on mineral surfaces. Elucidation of the mechanism of formation of these aggregates is important for an understanding of the interactions of HS in soils arid natural waters. The HS are formed mainly by enzymatic depolymerization and oxidation of plant biopolymers. These reactions transform the aromatic and lipid plant components into amphiphilic molecules, that is, molecules that consist of separate hydrophobic (nonpolar) and hydrophilic (polar) parts. The nonpolar parts of the molecules are composed of relatively unaltered segments of plant polymers and the polar parts of carboxylic acid groups. These amphiphiles form membrane-like aggregates on mineral surfaces and micelle-like aggregates in solution. The exterior surfaces of these aggregates are hydrophilic, and the interiors constitute separate hydrophobic liquid-like phases.

Holographic Characterization of Colloidal Fractal Aggregates

NASA Astrophysics Data System (ADS)

Wang, Chen; Cheong, Fook Chiong; Ruffner, David B.; Zhong, Xiao; Ward, Michael D.; Grier, David G.

In-line holographic microscopy images of micrometer-scale fractal aggregates can be interpreted with the Lorenz-Mie theory of light scattering and an effective-sphere model to obtain each aggregate's size and the population-averaged fractal dimension. We demonstrate this technique experimentally using model fractal clusters of polystyrene nanoparticles and fractal protein aggregates composed of bovine serum albumin and bovine pancreas insulin. This technique can characterize several thousand aggregates in ten minutes and naturally distinguishes aggregates from contaminants such as silicone oil droplets. Work supported by the SBIR program of the NSF.

Formation and structure of stable aggregates in binary diffusion-limited cluster-cluster aggregation processes

NASA Astrophysics Data System (ADS)

López-López, J. M.; Moncho-Jordá, A.; Schmitt, A.; Hidalgo-Álvarez, R.

2005-09-01

Binary diffusion-limited cluster-cluster aggregation processes are studied as a function of the relative concentration of the two species. Both, short and long time behaviors are investigated by means of three-dimensional off-lattice Brownian Dynamics simulations. At short aggregation times, the validity of the Hogg-Healy-Fuerstenau approximation is shown. At long times, a single large cluster containing all initial particles is found to be formed when the relative concentration of the minority particles lies above a critical value. Below that value, stable aggregates remain in the system. These stable aggregates are composed by a few minority particles that are highly covered by majority ones. Our off-lattice simulations reveal a value of approximately 0.15 for the critical relative concentration. A qualitative explanation scheme for the formation and growth of the stable aggregates is developed. The simulations also explain the phenomenon of monomer discrimination that was observed recently in single cluster light scattering experiments.

Observing Convective Aggregation

NASA Astrophysics Data System (ADS)

Holloway, Christopher E.; Wing, Allison A.; Bony, Sandrine; Muller, Caroline; Masunaga, Hirohiko; L'Ecuyer, Tristan S.; Turner, David D.; Zuidema, Paquita

2017-11-01

Convective self-aggregation, the spontaneous organization of initially scattered convection into isolated convective clusters despite spatially homogeneous boundary conditions and forcing, was first recognized and studied in idealized numerical simulations. While there is a rich history of observational work on convective clustering and organization, there have been only a few studies that have analyzed observations to look specifically for processes related to self-aggregation in models. Here we review observational work in both of these categories and motivate the need for more of this work. We acknowledge that self-aggregation may appear to be far-removed from observed convective organization in terms of time scales, initial conditions, initiation processes, and mean state extremes, but we argue that these differences vary greatly across the diverse range of model simulations in the literature and that these comparisons are already offering important insights into real tropical phenomena. Some preliminary new findings are presented, including results showing that a self-aggregation simulation with square geometry has too broad distribution of humidity and is too dry in the driest regions when compared with radiosonde records from Nauru, while an elongated channel simulation has realistic representations of atmospheric humidity and its variability. We discuss recent work increasing our understanding of how organized convection and climate change may interact, and how model discrepancies related to this question are prompting interest in observational comparisons. We also propose possible future directions for observational work related to convective aggregation, including novel satellite approaches and a ground-based observational network.

What favors convective aggregation and why?

NASA Astrophysics Data System (ADS)

Muller, Caroline; Bony, Sandrine

2015-07-01

The organization of convection is ubiquitous, but its physical understanding remains limited. One particular type of organization is the spatial self-aggregation of convection, taking the form of cloud clusters, or tropical cyclones in the presence of rotation. We show that several physical processes can give rise to self-aggregation and highlight the key features responsible for it, using idealized simulations. Longwave radiative feedbacks yield a "radiative aggregation." In that case, sufficient spatial variability of radiative cooling rates yields a low-level circulation, which induces the upgradient energy transport and radiative-convective instability. Not only do vertically integrated radiative budgets matter but the vertical profile of cooling is also crucial. Convective aggregation is facilitated when downdrafts below clouds are weak ("moisture-memory aggregation"), and this is sufficient to trigger aggregation in the absence of longwave radiative feedbacks. These results shed some light on the sensitivity of self-aggregation to various parameters, including resolution or domain size.

Lightweight aggregate abrasion study.

DOT National Transportation Integrated Search

1963-02-01

The rapid increase in the use of lightweight aggregates in structural concrete has created a number of problems for the Materials Engineer in evaluating this type aggregate. Exhaustive studies are being made of a number of properties of lightweight a...

Bouncing behavior of microscopic dust aggregates

NASA Astrophysics Data System (ADS)

Seizinger, A.; Kley, W.

2013-03-01

Context. Bouncing collisions of dust aggregates within the protoplanetary disk may have a significant impact on the growth process of planetesimals. Yet, the conditions that result in bouncing are not very well understood. Existing simulations studying the bouncing behavior used aggregates with an artificial, very regular internal structure. Aims: Here, we study the bouncing behavior of sub-mm dust aggregates that are constructed applying different sample preparation methods. We analyze how the internal structure of the aggregate alters the collisional outcome and we determine the influence of aggregate size, porosity, collision velocity, and impact parameter. Methods: We use molecular dynamics simulations where the individual aggregates are treated as spheres that are made up of several hundred thousand individual monomers. The simulations are run on graphic cards (GPUs). Results: Statistical bulk properties and thus bouncing behavior of sub-mm dust aggregates depend heavily on the preparation method. In particular, there is no unique relation between the average volume filling factor and the coordination number of the aggregate. Realistic aggregates bounce only if their volume filling factor exceeds 0.5 and collision velocities are below 0.1 ms-1. Conclusions: For dust particles in the protoplanetary nebula we suggest that the bouncing barrier may not be such a strong handicap in the growth phase of dust agglomerates, at least in the size range of ≈100 μm.

Curcumin inhibits aggregation of alpha-synuclein.

PubMed

Pandey, Neeraj; Strider, Jeffrey; Nolan, William C; Yan, Sherry X; Galvin, James E

2008-04-01

Aggregation of amyloid-beta protein (Abeta) is a key pathogenic event in Alzheimer's disease (AD). Curcumin, a constituent of the Indian spice Turmeric is structurally similar to Congo Red and has been demonstrated to bind Abeta amyloid and prevent further oligomerization of Abeta monomers onto growing amyloid beta-sheets. Reasoning that oligomerization kinetics and mechanism of amyloid formation are similar in Parkinson's disease (PD) and AD, we investigated the effect of curcumin on alpha-synuclein (AS) protein aggregation. In vitro model of AS aggregation was developed by treatment of purified AS protein (wild-type) with 1 mM Fe3+ (Fenton reaction). It was observed that the addition of curcumin inhibited aggregation in a dose-dependent manner and increased AS solubility. The aggregation-inhibiting effect of curcumin was next investigated in cell culture utilizing catecholaminergic SH-SY5Y cell line. A model system was developed in which the red fluorescent protein (DsRed2) was fused with A53T mutant of AS and its aggregation examined under different concentrations of curcumin. To estimate aggregation in an unbiased manner, a protocol was developed in which the images were captured automatically through a high-throughput cell-based screening microscope. The obtained images were processed automatically for aggregates within a defined dimension of 1-6 microm. Greater than 32% decrease in mutant alpha-synuclein aggregation was observed within 48 h subsequent to curcumin addition. Our data suggest that curcumin inhibits AS oligomerization into higher molecular weight aggregates and therefore should be further explored as a potential therapeutic compound for PD and related disorders.

Effects of earthworms and plants on the soil structure, the physical stabilization of soil organic matter and the microbial abundance and diversity in soil aggregates in a long term study

NASA Astrophysics Data System (ADS)

Zangerlé, Anne; Hissler, Christophe; Lavelle, Patrick

2014-05-01

Earthworms and plant roots, as ecosystem engineers, have large effects on biotic and abiotic properties of the soil system. They create biogenic soil macroaggregates (i.e. earthworm casts and root macroaggregates) with specific physical, chemical and microbiological properties. Research to date has mainly considered their impacts in isolation thereby ignoring potential interactions between these organisms. On the other hand, most of the existing studies focused on short to midterm time scale. We propose in this study to consider effect of earthworms and plants on aggregate dynamics at long time scale. A 24 months macrocosm experiment, under semi-controlled conditions, was conducted to assess the impacts of corn and endogeic plus anecic earthworms (Apporectodea caliginosa and Lumbricus terrestris) on soil structure, C stabilization and microbial abundance and biodiversity. Aggregate stability was assessed by wet-sieving. Macroaggregates (>2 mm) were also visually separated according to their biological origin (e.g., earthworms, roots). Total C and N contents were measured in aggregates of all size classes and origins. Natural abundances of 13C of corn, a C4 plant, were used as a supplemental marker of OM incorporation in aggregates. The genetic structure and the abundance of the bacterial and fungal communities were characterized by using respectively the B- and F-ARISA fingerprinting approach and quantitative PCR bacteria (341F/515R) and fungi (FF330/FR1). They significantly impacted the soil physical properties in comparison to the other treatments: lower bulk density in the first 10cm of the soil with 0.95 g/cm3 in absence of corn plants and 0.88 g/cm3 in presence of corn plants compared to control soil (1.21g/cm3). The presence of earthworms increased aggregate stability (mean weight diameter) by 7.6 %, while plants alone had no simple impacts on aggregation. A significant interaction revealed that earthworms increased aggregate stability in the presence of

Mesoporous Silica Nanoparticles-Encapsulated Agarose and Heparin as Anticoagulant and Resisting Bacterial Adhesion Coating for Biomedical Silicone.

PubMed

Wu, Fan; Xu, Tingting; Zhao, Guangyao; Meng, Shuangshuang; Wan, Mimi; Chi, Bo; Mao, Chun; Shen, Jian

2017-05-30

Silicone catheter has been widely used in peritoneal dialysis. The research missions of improving blood compatibility and the ability of resisting bacterial adhesion of silicone catheter have been implemented for the biomedical requirements. However, most of modification methods of surface modification were only able to develop the blood-contacting biomaterials with good hemocompatibility. It is difficult for the biomaterials to resist bacterial adhesion. Here, agarose was selected to resist bacterial adhesion, and heparin was chosen to improve hemocompatibility of materials. Both of them were loaded into mesoporous silica nanoparticles (MSNs), which were successfully modified on the silicone film surface via electrostatic interaction. Structures of the mesoporous coatings were characterized in detail by dynamic light scattering, transmission electron microscopy, Brunauer-Emmett-Teller surface area, thermogravimetric analysis, Fourier transform infrared spectroscopy, scanning electron microscope, and water contact angle. Platelet adhesion and aggregation, whole blood contact test, hemolysis and related morphology test of red blood cells, in vitro clotting time tests, and bacterial adhesion assay were performed to evaluate the anticoagulant effect and the ability of resisting bacterial adhesion of the modified silicone films. Results indicated that silicone films modified by MSNs had a good anticoagulant effect and could resist bacterial adhesion. The modified silicone films have potential as blood-contacting biomaterials that were attributed to their biomedical properties.

Bacterial communities associated with Porites white patch syndrome (PWPS) on three western Indian Ocean (WIO) coral reefs.

PubMed

Séré, Mathieu G; Tortosa, Pablo; Chabanet, Pascale; Turquet, Jean; Quod, Jean-Pascal; Schleyer, Michael H

2013-01-01

The scleractinian coral Porites lutea, an important reef-building coral on western Indian Ocean reefs (WIO), is affected by a newly-reported white syndrome (WS) the Porites white patch syndrome (PWPS). Histopathology and culture-independent molecular techniques were used to characterise the microbial communities associated with this emerging disease. Microscopy showed extensive tissue fragmentation generally associated with ovoid basophilic bodies resembling bacterial aggregates. Results of 16S rRNA sequence analysis revealed a high variability between bacterial communities associated with PWPS-infected and healthy tissues in P. lutea, a pattern previously reported in other coral diseases such as black band disease (BBD), white band disease (WBD) and white plague diseases (WPD). Furthermore, substantial variations in bacterial communities were observed at the different sampling locations, suggesting that there is no strong bacterial association in Porites lutea on WIO reefs. Several sequences affiliated with potential pathogens belonging to the Vibrionaceae and Rhodobacteraceae were identified, mainly in PWPS-infected coral tissues. Among them, only two ribotypes affiliated to Shimia marina (NR043300.1) and Vibrio hepatarius (NR025575.1) were consistently found in diseased tissues from the three geographically distant sampling localities. The role of these bacterial species in PWPS needs to be tested experimentally.

Applications of aggregation theory to sustainability assessment

DOE PAGES

Pollesch, N.; Dale, V. H.

2015-04-01

In order to aid in transition towards operations that promote sustainability goals, researchers and stakeholders use sustainability assessments. Although assessments take various forms, many utilize diverse sets of indicators that can number anywhere from two to over 2000. Indices, composite indicators, or aggregate values are used to simplify high dimensional and complex data sets and to clarify assessment results. Although the choice of aggregation function is a key component in the development of the assessment, there are few examples to be found in literature to guide appropriate aggregation function selection. This paper develops a connection between the mathematical study ofmore » aggregation functions and sustainability assessment in order to aid in providing criteria for aggregation function selection. Relevant mathematical properties of aggregation functions are presented and interpreted. Lastly, we provide cases of these properties and their relation to previous sustainability assessment research. Examples show that mathematical aggregation properties can be used to address the topics of compensatory behavior and weak versus strong sustainability, aggregation of data under varying units of measurements, multiple site multiple indicator aggregation, and the determination of error bounds in aggregate output for normalized and non-normalized indicator measures.« less

Familial aggregation analysis of gene expressions

PubMed Central

Rao, Shao-Qi; Xu, Liang-De; Zhang, Guang-Mei; Li, Xia; Li, Lin; Shen, Gong-Qing; Jiang, Yang; Yang, Yue-Ying; Gong, Bin-Sheng; Jiang, Wei; Zhang, Fan; Xiao, Yun; Wang, Qing K

2007-01-01

Traditional studies of familial aggregation are aimed at defining the genetic (and non-genetic) causes of a disease from physiological or clinical traits. However, there has been little attempt to use genome-wide gene expressions, the direct phenotypic measures of genes, as the traits to investigate several extended issues regarding the distributions of familially aggregated genes on chromosomes or in functions. In this study we conducted a genome-wide familial aggregation analysis by using the in vitro cell gene expressions of 3300 human autosome genes (Problem 1 data provided to Genetic Analysis Workshop 15) in order to answer three basic genetics questions. First, we investigated how gene expressions aggregate among different types (degrees) of relative pairs. Second, we conducted a bioinformatics analysis of highly familially aggregated genes to see how they are distributed on chromosomes. Third, we performed a gene ontology enrichment test of familially aggregated genes to find evidence to support their functional consensus. The results indicated that 1) gene expressions did aggregate in families, especially between sibs. Of 3300 human genes analyzed, there were a total of 1105 genes with one or more significant (empirical p < 0.05) familial correlation; 2) there were several genomic hot spots where highly familially aggregated genes (e.g., the chromosome 6 HLA genes cluster) were clustered; 3) as we expected, gene ontology enrichment tests revealed that the 1105 genes were aggregating not only in families but also in functional categories. PMID:18466548

Discrete stochastic charging of aggregate grains

NASA Astrophysics Data System (ADS)

Matthews, Lorin S.; Shotorban, Babak; Hyde, Truell W.

2018-05-01

Dust particles immersed in a plasma environment become charged through the collection of electrons and ions at random times, causing the dust charge to fluctuate about an equilibrium value. Small grains (with radii less than 1 μm) or grains in a tenuous plasma environment are sensitive to single additions of electrons or ions. Here we present a numerical model that allows examination of discrete stochastic charge fluctuations on the surface of aggregate grains and determines the effect of these fluctuations on the dynamics of grain aggregation. We show that the mean and standard deviation of charge on aggregate grains follow the same trends as those predicted for spheres having an equivalent radius, though aggregates exhibit larger variations from the predicted values. In some plasma environments, these charge fluctuations occur on timescales which are relevant for dynamics of aggregate growth. Coupled dynamics and charging models show that charge fluctuations tend to produce aggregates which are much more linear or filamentary than aggregates formed in an environment where the charge is stationary.

Use of functional gene expression and respirometry to study wastewater nitrification activity after exposure to low doses of copper.

PubMed

Kapoor, Vikram; Li, Xuan; Chandran, Kartik; Impellitteri, Christopher A; Santo Domingo, Jorge W

2016-04-01

Autotrophic nitrification in biological nitrogen removal systems has been shown to be sensitive to the presence of heavy metals in wastewater treatment plants. Using transcriptase-quantitative polymerase chain reaction (RT-qPCR) data, we examined the effect of copper on the relative expression of functional genes (i.e., amoA, hao, nirK, and norB) involved in redox nitrogen transformation in batch enrichment cultures obtained from a nitrifying bioreactor operated as a continuous reactor (24-h hydraulic retention time). 16S ribosomal RNA (rRNA) gene next-generation sequencing showed that Nitrosomonas-like populations represented 60-70% of the bacterial community, while other nitrifiers represented <5%. We observed a strong correspondence between the relative expression of amoA and hao and ammonia removal in the bioreactor. There were no considerable changes in the transcript levels of amoA, hao, nirK, and norB for nitrifying samples exposed to copper dosages ranging from 0.01 to 10 mg/L for a period of 12 h. Similar results were obtained when ammonia oxidation activity was measured via specific oxygen uptake rate (sOUR). The lack of nitrification inhibition by copper at doses lower than 10 mg/L may be attributed to the role of copper as cofactor for ammonia monooxygenase or to the sub-inhibitory concentrations of copper used in this study. Overall, these results demonstrate the use of molecular methods combined with conventional respirometry assays to better understand the response of wastewater nitrifying systems to the presence of copper.

Prediction of the aggregation propensity of proteins from the primary sequence: aggregation properties of proteomes.

PubMed

Castillo, Virginia; Graña-Montes, Ricardo; Sabate, Raimon; Ventura, Salvador

2011-06-01

In the cell, protein folding into stable globular conformations is in competition with aggregation into non-functional and usually toxic structures, since the biophysical properties that promote folding also tend to favor intermolecular contacts, leading to the formation of β-sheet-enriched insoluble assemblies. The formation of protein deposits is linked to at least 20 different human disorders, ranging from dementia to diabetes. Furthermore, protein deposition inside cells represents a major obstacle for the biotechnological production of polypeptides. Importantly, the aggregation behavior of polypeptides appears to be strongly influenced by the intrinsic properties encoded in their sequences and specifically by the presence of selective short regions with high aggregation propensity. This allows computational methods to be used to analyze the aggregation properties of proteins without the previous requirement for structural information. Applications range from the identification of individual amyloidogenic regions in disease-linked polypeptides to the analysis of the aggregation properties of complete proteomes. Herein, we review these theoretical approaches and illustrate how they have become important and useful tools in understanding the molecular mechanisms underlying protein aggregation. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Pyrite discs in coal: evidence for fossilized bacterial colonies

USGS Publications Warehouse

Southam, G.; Donald, R.; Rostad, A.; Brock, C.

2001-01-01

Discs of pyrite from 1 to 3 mm in diameter and ∼100 μm thick were observed within fracture planes in coal from the Black Mesa coal deposit in northeastern Arizona. The pyrite discs were composed of aggregates of crystals, which suggested that sulfide mineral diagenesis had initiated at multiple nucleation sites and occurred prior to the compaction forces occurring during coal formation. Stable sulfur isotope analysis of the discs (δ34S = −31.7‰) supports a bacterial origin resulting from dissimilatory sulfate reduction. Fossilized bacteria on the disc surfaces (average = 27/100 μm2) appeared as halos when viewed using reflected light microscopy, but were lenticular by scanning electron microscopy, each microfossil being 2–3 μm in length. A fossilized bacterial colony (pyrite disc), 1 mm in diameter, would contain ∼2.1 × 107 microfossils. These microfossils were not observed on hydrothermal pyrite. Coating and in-filling of sulfate-reducing bacteria with iron disulfide during in vitro sulfide mineral diagenesis provide mechanisms to explain the preservation of the three-dimensional lenticular microfossils observed on the pyrite discs.

Understanding curcumin-induced modulation of protein aggregation.

PubMed

Ahmad, Basir; Borana, Mohanish S; Chaudhary, Ankur P

2017-07-01

Curcumin, a diarylheptanoid compound, found in spice turmeric is known to alter the aggregation of proteins and reduce the toxicity of the aggregates. This review looks at the molecular basis of modulating protein aggregation and toxicity of the aggregates. Foremost, we identify the interaction of curcumin and its derivatives with proteins/peptides and the effect of their interaction on the conformational stability and unfolding/folding pathway(s). The unfolding/folding processes generate partially folded/unfolded intermediate, which serve as aggregation precursor state. Secondly, we discuss the effect of curcumin binding on the kinetics parameters of the aggregation process, which give information about the mechanism of the aggregation inhibition. We describe, in addition, that curcumin can accelerate/promote fibril formation by binding to oligomeric intermediate(s) accumulated in the aggregation pathway. Finally, we discuss the correlation of curcumin-induced monomeric and/or oligomeric precursor states with aggregate structure and toxicity. On the basis of these discussions, we propose a model describing curcumin-induced inhibition/promotion of formation of amyloid-like fibrils. Copyright © 2016 Elsevier B.V. All rights reserved.

Solubility and bacterial sealing ability of MTA and root-end filling materials.

PubMed

Espir, Camila Galletti; Guerreiro-Tanomaru, Juliane Maria; Spin-Neto, Rubens; Chávez-Andrade, Gisselle Moraima; Berbert, Fabio Luiz Camargo Villela; Tanomaru-Filho, Mario

2016-04-01

Objective To evaluate solubility and sealing ability of Mineral Trioxide Aggregate (MTA) and root-end filling materials. Material and Methods The materials evaluated were: MTA, Calcium Silicate Cement with zirconium oxide (CSC/ZrO2), and zinc oxide/eugenol (ZOE). Solubility test was performed according to ANSI/ADA. The difference between initial and final mass of the materials was analyzed after immersion in distilled water for 7 and 30 days. Retrograde cavities in human teeth with single straight root canal were performed by using ultrasonic tip CVD 9.5107-8. The cavities were filled with the evaluated materials to evaluate sealing ability using the bacterial leakage test with Enterococcus faecalis. Bacterial leakage was evaluated every 24 hours for six weeks observing the turbidity of Brain Heart infusion (BHI) medium in contact with root apex. Data were submitted to ANOVA followed by Tukey tests (solubility), and Kruskal-Wallis and Dunn tests (sealing ability) at a 5% significance level. Results For the 7-day period, ZOE presented highest solubility when compared with the other groups (p<0.05). For the 30-day period, no difference was observed among the materials. Lower bacterial leakage was observed for MTA and CSC/ZrO2, and both presented better results than ZOE (p<0.05). Conclusion MTA and CSC/ZrO2 presented better bacterial sealing capacity, which may be related to lower initial solubility observed for these materials in relation to ZOE.

Transportation and utilization of aggregates for road construction

NASA Astrophysics Data System (ADS)

Fladvad, Marit; Wigum, Børge Johannes; Aurstad, Joralf

2017-04-01

Road construction relies on non-renewable aggregate resources as the main construction material. Sources for high-quality aggregate resources are scattered, and requirements for aggregate quality can cause long transport distances between quarry and road construction site. In European countries, the average aggregate consumption per capita is 5 tonnes per year (European Aggregates Association, 2016), while the corresponding figure for Norway is 11 tonnes (Neeb, 2015). Half the Norwegian aggregate production (sand, gravel and crushed rock) is used for road construction. In Norway, aggregate resources have been considered abundant. However, stricter requirement for aggregate quality, and increased concern for sustainability and environmental issues have spurred focus on reduction of transport lengths through better utilization of local aggregate materials. In this research project, information about pavement design and aggregate quality requirements were gathered from a questionnaire sent to selected experts from the World Road Organization (PIARC), European Committee for Standardization (CEN), and Nordic Road Association (NVF). The gathered data was compared to identify differences and similarities for aggregate use in the participating countries. Further, the data was compared to known data from Norway regarding: - amount of aggregates required for a road structure - aggregate transport lengths and related costs A total of 18 countries participated in the survey, represented by either road authorities, research institutions, or contractors. There are large variations in practice for aggregate use among the represented countries, and the selection of countries is sufficient to illustrate a variety in pavement designs, aggregate sizes, and quality requirements for road construction. There are considerable differences in both pavement thickness and aggregate sizes used in the studied countries. Total thicknesses for pavement structures varies from 220 mm to 2400 mm

[Phylogenetic analysis and nitrogen removal characteristics of a heterotrophic nitrifying-aerobic denitrifying bacteria strain from marine environment].

PubMed

Sun, Xuemei; Li, Qiufen; Zhang, Yan; Liu, Huaide; Zhao, Jun; Qu, Keming

2012-06-04

We determined the phylogenetic position of a heterotrophic nitrifying-aerobic denitrifying bacterium X3, and detected its nitrogen removal characteristics for providing evidence to explain the principle of heterotrophic nitrification-aerobic denitrification and to improve the process in purification of marine-culture wastewater. The evolutionary position of the strain was determined based on its morphological, physiological, biochemical characteristics and 16SrRNA gene sequence. The nitrification-denitrification ability of this strain was detected by detecting its nitrogen removal efficiency and growth on different inorganic nitrogen source. Strain X3 was identified as Halomonas sp. It grew optimally at salinity 3%, pH 8.5, C:N 10:1 at 28 degrees C, and it could still survive at 15% salinity. The removal of NH4+ -N, NO2(-) -N and NO3(-) -N was 98.29%, 99.07%, 96.48% respectively within 24 h. When three inorganic nitrogen existed simultaneously, it always utilized ammonia firstly, and the total inorganic nitrogen removal was higher than with only one nitrogen, suggesting that strain X3 has the ability of simultaneous nitrification and denitrification and completing the whole nitrogen removing process. Strain X3 belonged to the genus of Halomonas. It had strong simultaneous nitrification and denitrification capability and could live in high-salinity environment.

Reusing recycled aggregates in structural concrete

NASA Astrophysics Data System (ADS)

Kou, Shicong

The utilization of recycled aggregates in concrete can minimize environmental impact and reduce the consumption of natural resources in concrete applications. The aim of this thesis is to provide a scientific basis for the possible use of recycled aggregates in structure concrete by conducting a comprehensive programme of laboratory study to gain a better understanding of the mechanical, microstructure and durability properties of concrete produced with recycled aggregates. The study also explored possible techniques to of improve the properties of recycled aggregate concrete that is produced with high percentages (≧ 50%) of recycled aggregates. These techniques included: (a) using lower water-to-cement ratios in the concrete mix design; (b) using fly ash as a cement replacement or as an additional mineral admixture in the concrete mixes, and (c) precasting recycled aggregate concrete with steam curing regimes. The characteristics of the recycled aggregates produced both from laboratory and a commercially operated pilot construction and demolition (C&D) waste recycling plant were first studied. A mix proportioning procedure was then established to produce six series of concrete mixtures using different percentages of recycled coarse aggregates with and without the use of fly ash. The water-to-cement (binder) ratios of 0.55, 0.50, 0.45 and 0.40 were used. The fresh properties (including slump and bleeding) of recycled aggregate concrete (RAC) were then quantified. The effects of fly ash on the fresh and hardened properties of RAC were then studied and compared with those RAC prepared with no fly ash addition. Furthermore, the effects of steam curing on the hardened properties of RAC were investigated. For micro-structural properties, the interfacial transition zones of the aggregates and the mortar/cement paste were analyzed by SEM and EDX-mapping. Moreover, a detailed set of results on the fracture properties for RAC were obtained. Based on the experimental

Bacterial oxidation of methyl bromide in fumigated agricultural soils

USGS Publications Warehouse

Miller, L.G.; Connell, T.L.; Guidetti, J.R.; Oremland, R.S.

1997-01-01

The oxidation of [14C]methyl bromide ([14C]MeBr) to 14CO2 was measured in field experiments with soils collected from two strawberry plots fumigated with mixtures of MeBr and chloropicrin (CCI3NO2). Although these fumigants are considered potent biocides, we found that the highest rates of MeBr oxidation occurred 1 to 2 days after injection when the fields were tarped, rather than before or several days after injection. No oxidation of MeBr occurred in heat-killed soils, indicating that microbes were the causative agents of the oxidation. Degradation of MeBr by chemical and/or biological processes accounted for 20 to 50% of the loss of MeBr during fumigation, with evasion to the atmosphere inferred to comprise the remainder. In laboratory incubations, complete removal of [14C]MeBr occurred within a few days, with 47 to 67% of the added MeBr oxidized to 14CO2 and the remainder of counts associated with the solid phase. Chloropicrin inhibited the oxidation of MeBr, implying that use of this substance constrains the extent of microbial degradation of MeBr during fumigation. Oxidation was by direct bacterial attack of MeBr and not of methanol, a product of the chemical hydrolysis of MeBr. Neither nitrifying nor methane-oxidizing bacteria were sufficiently active in these soils to account for the observed oxidation of MeBr, nor could the microbial degradation of MeBr be linked to cooxidation with exogenously supplied electron donors. However, repeated addition of MeBr to live soils resulted in higher rates of its removal, suggesting that soil bacteria used MeBr as an electron donor for growth. To support this interpretation, we isolated a gram-negative, aerobic bacterium from these soils which grew with MeBr as a sole source of carbon and energy.

Polyglutamine aggregation in Huntington and related diseases.

PubMed

Polling, Saskia; Hill, Andrew F; Hatters, Danny M

2012-01-01

Polyglutamine (polyQ)-expansions in different proteins cause nine neurodegenerative diseases. While polyQ aggregation is a key pathological hallmark of these diseases, how aggregation relates to pathogenesis remains contentious. In this chapter, we review what is known about the aggregation process and how cells respond and interact with the polyQ-expanded proteins. We cover detailed biophysical and structural studies to uncover the intrinsic features of polyQ aggregates and concomitant effects in the cellular environment. We also examine the functional consequences ofpolyQ aggregation and how cells may attempt to intervene and guide the aggregation process.

Effects of aggregation on the excitation dynamics of LH2 from Thermochromatium tepidum in aqueous phase and in chromatophores.

PubMed

Yang, Fan; Yu, Long-Jiang; Wang, Peng; Ai, Xi-Cheng; Wang, Zheng-Yu; Zhang, Jian-Ping

2011-06-23

We carried out femtosecond magic-angle and polarized pump-probe spectroscopies for the light-harvesting complex 2 (LH2) from Thermochromatium (Tch.) tepidum in aqueous phase and in chromatophores. To examine the effects of LH2 aggregation on the dynamics of excitation energy transfer, dominant monodispersed and aggregated LH2s were prepared by controlling the surfactant concentrations. The aqueous preparations solubilized with different concentrations of n-dodecyl-β-D-maltoside (DDM) show similar visible-to-near-infrared absorption spectra, but distinctively different aggregation states, as revealed by using dynamic light scattering. The B800 → B850 intra-LH2 energy transfer time was determined to be 1.3 ps for isolated LH2, which, upon aggregation in aqueous phase or clustering in chromatophores, shortened to 1.1 or 0.9 ps, respectively. The light-harvesting complex 1 (LH1) of this thermophilic purple sulfur bacterium contains bacteriochlorophyll a absorbing at 915 nm (B915), and the LH2(B850) → LH1(B915) intercomplex transfer time in chromatophores was found to be 6.6 ps. For chromatophores, a depolarization time of 21 ps was derived from the anisotropy kinetics of B850*, which is attributed to the migration of B850* excitation before being trapped by LH1. In addition, the B850* annihilation is accelerated upon LH2 aggregation in aqueous phase, but it is much less severe upon LH2 clustering in the intracytoplasmic membrane. These results are helpful in understanding the light-harvesting function of a bacterial photosynthetic membrane incorporating different types of antenna complexes.

Capping a Pulpotomy with Calcium Aluminosilicate Cement: Comparison to Mineral Trioxide Aggregates

PubMed Central

Kramer, Phillip R.; Woodmansey, Karl F.; White, Robert; Primus, Carolyn M.; Opperman, Lynne A.

2014-01-01

Introduction Calcium aluminate cements have shown little affinity for bacterial growth, low toxicity, and immunogenicity when used as a restoration material, but calcium aluminate cements have not been tested in vivo in pulpotomy procedures. Methods To address this question, a calcium aluminate cement (Quick-Set) was tested along with 2 mineral trioxide aggregates, ProRoot MTA and MTA Plus. These cements were used as a capping agent after pulpotomy. Control rats had no pulpotomy, or the pulpotomy was not capped. Proinflammatory cytokines interleukin (IL)-1β and IL-1α were measured, and histology was performed at 30 and 60 days after capping. The nociceptive response was determined by measuring the lengthening of the rat's meal duration. Results and Conclusions: IL-1β and IL-1α concentrations were reduced in the capped teeth, but no differences were observed among the 3 cements. Dentinal bridging could be detected at both 30 and 60 days with each of the 3 cements, and the pulps were still vital 60 days after capping. Meal duration significantly shortened after placement of the 3 different cements, indicating a nociceptive response, but there were no differences among the materials. Calcium aluminate cements had similar properties to mineral trioxide aggregates and is a viable option for pulpotomy procedures. PMID:25146026

Excited-state dynamics of astaxanthin aggregates

NASA Astrophysics Data System (ADS)

Fuciman, Marcel; Durchan, Milan; Šlouf, Václav; Keşan, Gürkan; Polívka, Tomáš

2013-05-01

Astaxanthin forms three types of aggregates in hydrated dimethyl sulfoxide (DMSO). In DMSO/water ratio of 1:1, a red-shifted J-aggregate with maximum at 570 nm is generated, while a ratio of 1:9 produces blue-shifted H-aggregates with peaks at 386 nm (H1) and 460 nm (H2). Monomeric astaxanthin in DMSO has an S1 lifetime of 5.3 ps, but a long-lived (33 ps) S∗ signal was also identified. Aggregation changes the S1 lifetimes to 17 ps (H1), 30 ps (H2), and 14 ps (J). Triplet state of astaxanthin, most likely generated via singlet homofission, was observed in H1 and H2 aggregates.

Aggregation Kinetics of Hematite Particles in the Presence of Outer Membrane Cytochrome OmcA of Shewanella oneidenesis MR-1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sheng, Anxu; Liu, Feng; Shi, Liang

2016-09-20

The aggregation behavior of 9, 36, and 112 nm hematite particles was studied in the presence of OmcA, a bacterial extracellular protein, in aqueous dispersions at pH 5.7 through time-resolved dynamic light scattering, electrophoretic mobility, and circular dichroism spectra, respectively. At low salt concentration, the attachment efficiencies of hematite particles in all sizes first increased, then decreased, and finally remained stable with the increase of OmcA concentration, indicating the dominant interparticle interaction changed along with the increase in the protein-to-particle ratio. Nevertheless, at high salt concentration, the attachment efficiencies of all hematite samples gradually decreased with increasing OmcA concentration, whichmore » can be attributed to increasing steric force. Additionally, the aggregation behavior of OmcA-hematite conjugates was more correlated to total particle-surface area than primary particle size. It was further established that OmcA could stabilize hematite nanoparticles more efficiently than bovine serum albumin (BSA), a model plasma protein, due to the higher affinity of OmcA to hematite surface. This study highlighted the effects of particle properties, solution conditions, and protein properties on the complicated aggregation behavior of protein-nanoparticle conjugates in aqueous environments.« less

Biomass characteristics of two types of submerged membrane bioreactors for nitrogen removal from wastewater.

PubMed

Liang, Zhihua; Das, Atreyee; Beerman, Daniel; Hu, Zhiqiang

2010-06-01

Biomass characteristics and microbial community diversity between a submerged membrane bioreactor with mixed liquor recirculation (MLE/MBR) and a membrane bioreactor with the addition of integrated fixed biofilm medium (IFMBR) were compared for organic carbon and nitrogen removal from wastewater. The two bench-scale MBRs were continuously operated in parallel at a hydraulic retention time (HRT) of 24h and solids retention time (SRT) of 20d. Both MBRs demonstrated good COD removal efficiencies (>97.7%) at incremental inflow organic loading rates. The total nitrogen removal efficiencies were 67% for MLE/MBR and 41% for IFMBR. The recirculation of mixed liquor from aerobic zone to anoxic zone in the MLE/MBR resulted in higher microbial activities of heterotrophic (46.96mgO(2)/gVSSh) and autotrophic bacteria (30.37mgO(2)/gVSSh) in the MLE/MBR compared to those from IFMBR. Terminal Restriction Fragment Length Polymorphism analysis indicated that the higher nitrifying activities were correlated with more diversity of nitrifying bacterial populations in the MLE/MBR. Membrane fouling due to bacterial growth was evident in both the reactors. Even though the trans-membrane pressure and flux profiles of MLE/MBR and IFMBR were different, the patterns of total membrane resistance changes had no considerable difference under the same operating conditions. The results suggest that metabolic selection via alternating anoxic/aerobic processes has the potential of having higher bacterial activities and improved nutrient removal in MBR systems. Copyright 2010 Elsevier Ltd. All rights reserved.

Rigid aggregates: theory and applications

NASA Astrophysics Data System (ADS)

Richardson, D. C.

2005-08-01

Numerical models employing ``perfect'' self-gravitating rubble piles that consist of monodisperse rigid spheres with configurable contact dissipation have been used to explore collisional and rotational disruption of gravitational aggregates. Applications of these simple models include numerical simulations of planetesimal evolution, asteroid family formation, tidal disruption, and binary asteroid formation. These studies may be limited by the idealized nature of the rubble pile model, since perfect identical spheres stack and shear in a very specific, possibly over-idealized way. To investigate how constituent properties affect the overall characteristics of a gravitational aggregate, particularly its failure modes, we have generalized our numerical code to model colliding, self-gravitating, rigid aggregates made up of variable-size spheres. Euler's equation of rigid-body motion in the presence of external torques are implemented, along with a self-consistent prescription for handling non-central impacts. Simple rules for sticking and breaking are also included. Preliminary results will be presented showing the failure modes of gravitational aggregates made up of smaller, rigid, non-idealized components. Applications of this new capability include more realistic aggregate models, convenient modeling of arbitrary rigid shapes for studies of the stability of orbiting companions (replacing one or both bodies with rigid aggregates eliminates expensive interparticle collisions while preserving the shape, spin, and gravity field of the bodies), and sticky particle aggregation in dense planetary rings. This material is based upon work supported by the National Aeronautics and Space Administration under Grant No. NAG511722 issued through the Office of Space Science and by the National Science Foundation under Grant No. AST0307549.

Production of lightweight aggregates from washing aggregate sludge and fly ash

NASA Astrophysics Data System (ADS)

González-Corrochano, Beatriz; Alonso-Azcárate, Jacinto; Rodas, Magdalena

2010-05-01

Increasing generation of wastes is one of the main environmental problems in industrialised countries. Heat treatment at high temperatures can convert some types of wastes into ceramic products with a wide range of microstructural features and properties (Bethanis et al., 2004). A lightweight aggregate (LWA) is a granular material with a bulk density (bd) not exceeding 1.20 g/cm3 or with a particle density not exceeding 2.00 g/cm3 (UNE-EN-13055-1, 2003). They have become a focus of interest because the low particle density and the low bulk density entail a decrease in the load transmitted to the ground, and less work and effort are required to transport them (De' Gennaro et al., 2004). The benefits associated with these low densities, which are due to the formation of voids and pores, are very good thermal and acoustic insulation and materials with a good resistance to fire (Benbow, 1987; Fakhfakh et al., 2007). The objective was to recycle fly ash, used motor oil from cars and mineral wastes from washing aggregate sludge, in order to obtain a usable material such as lightweight aggregates, and also to ensure that they are of good quality for different applications. Raw materials have been physically, chemically and mineralogically characterized. On the basis of the results obtained, they were mixed, milled to a grain size of less than 200 μm (Yasuda, 1991), formed into pellets, pre-heated for 5 min and sintered in a rotary kiln at 1150°C, 1175°C, 1200°C and 1225°C for 10 and 15 min at each temperature (Theating). Effects of raw material characteristics, heating temperature and dwell time on the following LWAs properties were determined: loss on ignition (LOI), bloating index (BI), loose bulk density (bd), apparent and dry particle density (ad, dd), voids (H), water absorption (WA24h) and compressive strength (S). The products obtained were lightweight aggregates in accordance with norm UNE-EN-13055-1 (bd ≤1.20 g/cm3 or particle density ≤2.00 g/cm3). LWAs

Flow Partitioning in Fully Saturated Soil Aggregates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Xiaofan; Richmond, Marshall C.; Scheibe, Timothy D.

2014-03-30

Microbes play an important role in facilitating organic matter decomposition in soils, which is a major component of the global carbon cycle. Microbial dynamics are intimately coupled to environmental transport processes, which control access to labile organic matter and other nutrients that are needed for the growth and maintenance of microorganisms. Transport of soluble nutrients in the soil system is arguably most strongly impacted by preferential flow pathways in the soil. Since the physical structure of soils can be characterized as being formed from constituent micro aggregates which contain internal porosity, one pressing question is the partitioning of the flowmore » among the “inter-aggregate” and “intra-aggregate” pores and how this may impact overall solute transport within heterogeneous soil structures. The answer to this question is particularly important in evaluating assumptions to be used in developing upscaled simulations based on highly-resolved mechanistic models. We constructed a number of diverse multi-aggregate structures with different packing ratios by stacking micro-aggregates containing internal pores and varying the size and shape of inter-aggregate pore spacing between them. We then performed pore-scale flow simulations using computational fluid dynamics methods to determine the flow patterns in these aggregate-of-aggregates structures and computed the partitioning of the flow through intra- and inter-aggregate pores as a function of the spacing between the aggregates. The results of these numerical experiments demonstrate that soluble nutrients are largely transported via flows through inter-aggregate pores. Although this result is consistent with intuition, we have also been able to quantify the relative flow capacity of the two domains under various conditions. For example, in our simulations, the flow capacity through the aggregates (intra-aggregate flow) was less than 2% of the total flow when the spacing between the

Waves and aggregation patterns in myxobacteria

NASA Astrophysics Data System (ADS)

Igoshin, Oleg A.; Welch, Roy; Kaiser, Dale; Oster, George

2004-03-01

Under starvation conditions, a population of myxobacteria aggregates to build a fruiting body whose shape is species-specific and within which the cells sporulate. Early in this process, cells often pass through a "ripple phase" characterized by traveling linear, concentric, and spiral waves. These waves are different from the waves observed during slime mold aggregation that depend on diffusible morphogens, because myxobacteria communicate by direct contact. The difference is most dramatic when waves collide: rather than annihilating one another, myxobacterial waves appear to pass through one another unchanged. Under certain conditions, the spacing and location of the nascent fruiting bodies is determined by the wavelength and pattern of the waves. Later in fruiting body development, waves are replaced by streams of cells that circulate around small initial aggregates enlarging and rounding them. Still later, pairs of motile aggregates coalesce to form larger aggregates that develop into fruiting bodies. Here we present a mathematical model that quantitatively explains these wave and aggregation phenomena.

Structure-based inhibitors of tau aggregation

NASA Astrophysics Data System (ADS)

Seidler, P. M.; Boyer, D. R.; Rodriguez, J. A.; Sawaya, M. R.; Cascio, D.; Murray, K.; Gonen, T.; Eisenberg, D. S.

2018-02-01

Aggregated tau protein is associated with over 20 neurological disorders, which include Alzheimer's disease. Previous work has shown that tau's sequence segments VQIINK and VQIVYK drive its aggregation, but inhibitors based on the structure of the VQIVYK segment only partially inhibit full-length tau aggregation and are ineffective at inhibiting seeding by full-length fibrils. Here we show that the VQIINK segment is the more powerful driver of tau aggregation. Two structures of this segment determined by the cryo-electron microscopy method micro-electron diffraction explain its dominant influence on tau aggregation. Of practical significance, the structures lead to the design of inhibitors that not only inhibit tau aggregation but also inhibit the ability of exogenous full-length tau fibrils to seed intracellular tau in HEK293 biosensor cells into amyloid. We also raise the possibility that the two VQIINK structures represent amyloid polymorphs of tau that may account for a subset of prion-like strains of tau.

Macrophage triggering by aggregated immunoglobulins. II. Comparison of IgE and IgG aggregates or immune complexes.

PubMed Central

Pestel, J; Dessaint, J P; Joseph, M; Bazin, H; Capron, A

1984-01-01

Macrophages incubated with complexed or aggregated IgE released beta-glucuronidase (beta-G) within 30 min. In contrast in the presence of aggregated or complexed IgG, macrophages liberated equivalent amount of beta-G only after 6 h incubation. In addition the rapid macrophage stimulation induced by aggregated IgE was also followed by a faster 3H-glucosamine incorporation when compared to the delayed activation caused by aggregated IgG. However, macrophages stimulated either by IgG or by IgE oligomers produced the same percentage of plasminogen activator at 24 h. In contrast, while the interaction between macrophages and aggregated IgE was only followed by a peak of cyclic GMP and a beta-G release during the first 30 min of incubation, the interaction between macrophages and IgG oligomers was accompanied by a simultaneous increase of cyclic GMP and AMP nucleotides and by an absence of beta-G exocytosis. Moreover, the beta-G release induced by aggregated IgE was increased when macrophages were preincubated with aggregated IgG. This additive effect was not observed in the reverse situation. Finally macrophages activated by IgG oligomers were demonstrated to exert a cytotoxic effect on tumour cells and to kill schistosomula in the presence of a low level of complement. Taken together these results underline the peculiar ability of aggregated or complexed IgE to trigger rapidly the macrophage activation compared to aggregated IgG and can explain the important role of complexed IgE in some macrophage dependent cytotoxicity mechanisms (i.e. in parasitic diseases). PMID:6088135

Recovery of bioactive protein from bacterial inclusion bodies using trifluoroethanol as solubilization agent.

PubMed

Upadhyay, Vaibhav; Singh, Anupam; Jha, Divya; Singh, Akansha; Panda, Amulya K

2016-06-08

Formation of inclusion bodies poses a major hurdle in recovery of bioactive recombinant protein from Escherichia coli. Urea and guanidine hydrochloride have routinely been used to solubilize inclusion body proteins, but many times result in poor recovery of bioactive protein. High pH buffers, detergents and organic solvents like n-propanol have been successfully used as mild solubilization agents for high throughput recovery of bioactive protein from bacterial inclusion bodies. These mild solubilization agents preserve native-like secondary structures of proteins in inclusion body aggregates and result in improved recovery of bioactive protein as compared to conventional solubilization agents. Here we demonstrate solubilization of human growth hormone inclusion body aggregates using 30% trifluoroethanol in presence of 3 M urea and its refolding into bioactive form. Human growth hormone was expressed in E. coli M15 (pREP) cells in the form of inclusion bodies. Different concentrations of trifluoroethanol with or without addition of low concentration (3 M) of urea were used for solubilization of inclusion body aggregates. Thirty percent trifluoroethanol in combination with 3 M urea was found to be suitable for efficient solubilization of human growth hormone inclusion bodies. Solubilized protein was refolded by dilution and purified by anion exchange and size exclusion chromatography. Purified protein was analyzed for secondary and tertiary structure using different spectroscopic tools and was found to be bioactive by cell proliferation assay. To understand the mechanism of action of trifluoroethanol, secondary and tertiary structure of human growth hormone in trifluoroethanol was compared to that in presence of other denaturants like urea and guanidine hydrochloride. Trifluoroethanol was found to be stabilizing the secondary structure and destabilizing the tertiary structure of protein. Finally, it was observed that trifluoroethanol can be used to solubilize

Natural aggregates of the conterminous United States

USGS Publications Warehouse

Langer, William H.

1988-01-01

Crushed stone and sand and gravel are the two main sources of natural aggregates. These materials are commonly used construction materials and frequently can be interchanged with one another. They are widely used throughout the United States, with every State except two producing crushed stone. Together they amount to about half the mining volume in the United States. Approximately 96 percent of sand and gravel and 77 percent of the crushed stone produced in the United States are used in the construction industry. Natural aggregates are widely distributed throughout the United States in a variety of geologic environments. Sand and gravel deposits commonly are the results of the weathering of bedrock and subsequent transportation and deposition of the material by water or ice (glaciers). As such, they commonly occur as river or stream deposits or in glaciated areas as glaciofluvial and other deposits. Crushed stone aggregates are derived from a wide variety of parent bedrock materials. Limestone and other carbonates account for approximately three quarters of the rocks used for crushed stone, with granite and other igneous rocks making up the bulk of the remainder. Limestone deposits are widespread throughout the Central and Eastern United States and are scattered in the West. Granites are widely distributed in the Eastern and Western United States, with few exposures in the Midwest. Igneous rocks (excluding granites) are largely concentrated in the Western United States and in a few isolated localities in the East. Even though natural aggregates are widely distributed throughout the United States, they are not universally available for consumptive use. Some areas are devoid of sand and gravel, and potential sources of crushed stone may be covered with sufficient unconsolidated material to make surface mining impractical. In some areas many aggregates do not meet the physical property requirements for certain uses, or they may contain mineral constituents that react

24 CFR 58.32 - Project aggregation.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 24 Housing and Urban Development 1 2010-04-01 2010-04-01 false Project aggregation. 58.32 Section... Environmental Review Process: Documentation, Range of Activities, Project Aggregation and Classification § 58.32 Project aggregation. (a) A responsible entity must group together and evaluate as a single project all...

24 CFR 58.32 - Project aggregation.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 24 Housing and Urban Development 1 2011-04-01 2011-04-01 false Project aggregation. 58.32 Section... Environmental Review Process: Documentation, Range of Activities, Project Aggregation and Classification § 58.32 Project aggregation. (a) A responsible entity must group together and evaluate as a single project all...

24 CFR 58.32 - Project aggregation.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 24 Housing and Urban Development 1 2014-04-01 2014-04-01 false Project aggregation. 58.32 Section... Environmental Review Process: Documentation, Range of Activities, Project Aggregation and Classification § 58.32 Project aggregation. (a) A responsible entity must group together and evaluate as a single project all...

24 CFR 58.32 - Project aggregation.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 24 Housing and Urban Development 1 2012-04-01 2012-04-01 false Project aggregation. 58.32 Section... Environmental Review Process: Documentation, Range of Activities, Project Aggregation and Classification § 58.32 Project aggregation. (a) A responsible entity must group together and evaluate as a single project all...

Macroeconomic susceptibility, inflation, and aggregate supply

NASA Astrophysics Data System (ADS)

Hawkins, Raymond J.

2017-03-01

We unify aggregate-supply dynamics as a time-dependent susceptibility-mediated relationship between inflation and aggregate economic output. In addition to representing well various observations of inflation-output dynamics this parsimonious formalism provides a straightforward derivation of popular representations of aggregate-supply dynamics and a natural basis for economic-agent expectations as an element of inflation formation. Our formalism also illuminates questions of causality and time-correlation that challenge central banks for whom aggregate-supply dynamics is a key constraint in their goal of achieving macroeconomic stability.

Aggregation server for grid-integrated vehicles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kempton, Willett

2015-05-26

Methods, systems, and apparatus for aggregating electric power flow between an electric grid and electric vehicles are disclosed. An apparatus for aggregating power flow may include a memory and a processor coupled to the memory to receive electric vehicle equipment (EVE) attributes from a plurality of EVEs, aggregate EVE attributes, predict total available capacity based on the EVE attributes, and dispatch at least a portion of the total available capacity to the grid. Power flow may be aggregated by receiving EVE operational parameters from each EVE, aggregating the received EVE operational parameters, predicting total available capacity based on the aggregatedmore » EVE operational parameters, and dispatching at least a portion of the total available capacity to the grid.« less

Aggregated particles caused by instrument artifact

NASA Astrophysics Data System (ADS)

Pierce, Ashley M.; Loría-Salazar, S. Marcela; Arnott, W. Patrick; Edwards, Grant C.; Miller, Matthieu B.; Gustin, Mae S.

2018-04-01

Previous studies have indicated that superaggregates, clusters of aggregates of soot primary particles, can be formed in large-scale turbulent fires. Due to lower effective densities, higher porosity, and lower aerodynamic diameters, superaggregates may pass through inlets designed to remove particles < 2.5 µm in aerodynamic diameter (PM2.5). Ambient particulate matter samples were collected at Peavine Peak, NV, USA (2515 m) northwest of Reno, NV, USA from June to November 2014. The Teledyne Advanced Pollution Instrumentation (TAPI) 602 BetaPlus particulate monitor was used to collect PM2.5 on two filter types. During this time, aggregated particles > 2.5 µm in aerodynamic diameter were collected on 36 out of 158 sample days. On preliminary analysis, it was thought that these aggregated particles were superaggregates, depositing past PM10 (particles < 10 µm in aerodynamic diameter) pre-impactors and PM2.5 cyclones. However, further analysis revealed that these aggregated particles were dissimilar to superaggregates observed in previous studies, both in morphology and in elemental composition. To determine if the aggregated particles were superaggregates or an instrument artifact, samples were investigated for the presence of certain elements, the occurrence of fires, high relative humidity and wind speeds, as well as the use of generators on site. Samples with aggregated particles, referred to as aggregates, were analyzed using a scanning electron microscope for size and shape and energy dispersive X-ray spectroscopy was used for elemental analysis. It was determined, based on the high amounts of aluminum present in the aggregate samples, that a sampling artifact associated with the sample inlet and prolonged, high wind events was the probable reason for the observed aggregates.

Seasonal variability of soil aggregate stability

NASA Astrophysics Data System (ADS)

Rohoskova, M.; Kodesova, R.; Jirku, V.; Zigova, A.; Kozak, J.

2009-04-01

Seasonal variability of soil properties measured in surface horizons of three soil types (Haplic Luvisol, Greyic Phaeozem, Haplic Cambisol) was studied in years 2007 and 2008. Undisturbed and disturbed soil samples were taken every month to evaluate field water content, bulk density, porosity, ration of gravitational and capillary pores, pHKCl and pHH2O, organic matter content and its quality, aggregate stability using WSA index. In addition, micromorphological features of soil aggregates were studied in thin soil sections that were made from undisturbed large soil aggregates. Results showed that soil aggregate stability depended on stage of the root zone development, soil management and climatic conditions. Larger aggregate stabilities and also larger ranges of measure values were obtained in the year 2007 then those measured in 2008. This was probably caused by lower precipitations and consequently lower soil water contents observed in 2007 than those measured in 2008. The highest aggregate stability was measured at the end of April in the years 2007 and 2008 in Haplic Luvisol and Greyic Phaeozem, and at the end of June in the year 2007 and at the beginning of June in 2008 in Haplic Cambisol. In all cases aggregate stability increased during the root growth and then gradually decreased due to summer rainfall events. Aggregate stability reflected aggregate structure and soil pore system development, which was documented on micromorphological images and evaluated using the ration of gravitational and capillary pores measured on the undisturbed sol samples. Acknowledgement: Authors acknowledge the financial support of the Grant Agency of the Czech Republic grant No. 526/08/0434, and the Ministry of Education, Youth and Sports grant No. MSM 6046070901.

Aggregate R-R-V Analysis

EPA Pesticide Factsheets

The excel file contains time series data of flow rates, concentrations of alachlor , atrazine, ammonia, total phosphorus, and total suspended solids observed in two watersheds in Indiana from 2002 to 2007. The aggregate time series data corresponding or representative to all these parameters was obtained using a specialized, data-driven technique. The aggregate data is hypothesized in the published paper to represent the overall health of both watersheds with respect to various potential water quality impairments. The time series data for each of the individual water quality parameters were used to compute corresponding risk measures (Rel, Res, and Vul) that are reported in Table 4 and 5. The aggregation of the risk measures, which is computed from the aggregate time series and water quality standards in Table 1, is also reported in Table 4 and 5 of the published paper. Values under column heading uncertainty reports uncertainties associated with reconstruction of missing records of the water quality parameters. Long-term records of the water quality parameters were reconstructed in order to estimate the (R-R-V) and corresponding aggregate risk measures. This dataset is associated with the following publication:Hoque, Y., S. Tripathi, M. Hantush , and R. Govindaraju. Aggregate Measures of Watershed Health from Reconstructed Water Quality Data with Uncertainty. Ed Gregorich JOURNAL OF ENVIRONMENTAL QUALITY. American Society of Agronomy, MADISON, WI,

Reuse of industrial sludge as construction aggregates.

PubMed

Tay, J H; Show, K Y; Hong, S Y

2001-01-01

Industrial wastewater sludge and dredged marine clay are high volume wastes that needed enormous space at landfill disposal sites. Due to the limitation of land space, there is an urgent need for alternative disposal methods for these two wastes. This study investigates the possibility of using the industrial sludge in combination with marine clay as construction aggregates. Different proportions of sludge and clay were made into round and angular aggregates. It was found that certain mix proportions could provide aggregates of adequate strength, comparable to that of conventional aggregates. Concrete samples cast from the sludge-clay aggregates yield compressive strengths in the range of 31.0 to 39.0 N/mm2. The results showed that the round aggregates of 100% sludge and the crush aggregates of sludge with up to 20% clay produced concrete of compressive strengths which are superior to that of 38.0 N/mm2 for conventional aggregate. The study indicates that the conversion of high volume wastes into construction materials is a potential option for waste management.

Aggregated Computational Toxicology Online Resource

EPA Pesticide Factsheets

Aggregated Computational Toxicology Online Resource (AcTOR) is EPA's online aggregator of all the public sources of chemical toxicity data. ACToR aggregates data from over 1,000 public sources on over 500,000 chemicals and is searchable by chemical name, other identifiers and by chemical structure. It can be used to query a specific chemical and find all publicly available hazard, exposure and risk assessment data. It also provides access to EPA's ToxCast, ToxRefDB, DSSTox, Dashboard and DSSTox data.

An assessment of adhesion, aggregation and surface charges of Lactobacillus strains derived from the human oral cavity.

PubMed

Piwat, S; Sophatha, B; Teanpaisan, R

2015-07-01

There is limited information concerning the adhesion and aggregation of human oral lactobacilli. In this study, the adhesion of 10 Lactobacillus species was investigated using H357 oral keratinocyte cells as an in vitro model for oral mucosa. Coaggregation with the representative oral pathogen, Streptococcus mutans ATCC 25175, and the physicochemical cell properties was also evaluated. The results demonstrated significant variations in adhesion (42-96%) and aggregation (autoaggregation, 14-95%; coaggregation, 19-65%). All strains showed a high affinity for chloroform, and most strains had a moderate-to-high hydrophobicity. All strains, except Lactobacillus casei and Lactobacillus gasseri, showed a moderate affinity for ethyl acetate. There was a strong association of autoaggregation with coaggregation (rs = 0·883, P < 0·001). The highest mean for autoaggregation (74%) and coaggregation (47%) belonged to the Lact. gasseri strains. Correlations between the adhesion and surface characteristics and aggregation were observed among the Lactobacillus fermentum and Lactobacillus paracasei strains; however, there was a variation in the strains properties within and between species. This study indicated that the Lact. gasseri, Lact. fermentum, and Lact. paracasei strains might be potential probiotics for the human oral cavity given their desirable properties. It should also be emphasized that a selective process for probiotic strains is required. Adhesion to host tissues and bacterial aggregation (auto- and coaggregation) are the highly important criteria for selecting strains with probiotic potential. These abilities are commonly involved with surface-charged characteristics. This is the first study to investigate the oral Lactobacillus species using an oral keratinocyte cell line. Significant results were found for the correlations between the adhesion and surface charge characteristics and for aggregation among certain strains of Lactobacillus gasseri, Lactobacillus

Lightweight alumina refractory aggregate. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swansiger, T.G.; Pearson, A.

1996-07-16

Objective was to develop a lightweight, high alumina refractory aggregate for use in various high performance insulating (low thermal conductivity) refractory applications (e.g., in the aluminium, glass, cement, and iron and steel industries). A new aggregate process was developed through bench and pilot-scale experiments involving extrusion of a blend of calcined and activated alumina powders and organic extrusion aids and binders. The aggregate, with a bulk density approaching 2.5 g/cc, exhibited reduced thermal conductivity and adequate fired strength compared to dense tabular aggregate. Refractory manufacturers were moderately enthusiastic over the results. Alcoa prepared an economic analysis for producing lightweight aggregate,more » based on a retrofit of this process into existing Alcoa production facilities. However, a new, competing lightweight aggregate material was developed by another company; this material (Plasmal{trademark})had a significantly more favorable cost base than the Alcoa/DOE material, due to cheap raw materials and fewer processing steps. In late 1995, Alcoa became a distributor of Plasmal. Alcoa estimated that {ge}75% of the market originally envisioned for the Alcoa/DOE aggregate would be taken by Plasmal. Hence, it was decided to terminate the contract without the full- scale demonstration.« less

Inducing protein aggregation by extensional flow

PubMed Central

Dobson, John; Kumar, Amit; Willis, Leon F.; Tuma, Roman; Higazi, Daniel R.; Turner, Richard; Lowe, David C.; Ashcroft, Alison E.; Radford, Sheena E.; Kapur, Nikil

2017-01-01

Relative to other extrinsic factors, the effects of hydrodynamic flow fields on protein stability and conformation remain poorly understood. Flow-induced protein remodeling and/or aggregation is observed both in Nature and during the large-scale industrial manufacture of proteins. Despite its ubiquity, the relationships between the type and magnitude of hydrodynamic flow, a protein’s structure and stability, and the resultant aggregation propensity are unclear. Here, we assess the effects of a defined and quantified flow field dominated by extensional flow on the aggregation of BSA, β2-microglobulin (β2m), granulocyte colony stimulating factor (G-CSF), and three monoclonal antibodies (mAbs). We show that the device induces protein aggregation after exposure to an extensional flow field for 0.36–1.8 ms, at concentrations as low as 0.5 mg mL−1. In addition, we reveal that the extent of aggregation depends on the applied strain rate and the concentration, structural scaffold, and sequence of the protein. Finally we demonstrate the in situ labeling of a buried cysteine residue in BSA during extensional stress. Together, these data indicate that an extensional flow readily unfolds thermodynamically and kinetically stable proteins, exposing previously sequestered sequences whose aggregation propensity determines the probability and extent of aggregation. PMID:28416674

Locally available aggregate and sediment production

Treesearch

Randy B. Foltz; Mark Truebe

2003-01-01

Selection of suitable locally available materials to build strong and durable roads with aggregate surfaces is desired to minimize road construction and maintenance costs and to minimize the detrimental effects of sedimentation. Eighteen aggregates were selected from local sources in Idaho, Oregon, South Dakota, and Washington State. Aggregate was placed in shallow...

Contrasting self-aggregation over land and ocean surfaces

NASA Astrophysics Data System (ADS)

Inda Diaz, H. A.; O'Brien, T. A.

2017-12-01

The spontaneous organization of convection into clusters, or self-aggregation, demonstrably changes the nature and statistics of precipitation. While there has been much recent progress in this area, the processes that control self-aggregation are still poorly understood. Most of the work to date has focused on self-aggregation over ocean-like surfaces, but it is particularly pressing to understand what controls convective aggregation over land, since the associated change in precipitation statistics—between non-aggregated and aggregated convection—could have huge impacts on society and infrastructure. Radiative-convective equilibrium (RCE), has been extensively used as an idealized framework to study the tropical atmosphere. Self-aggregation manifests in numerous numerical models of RCE, nevertheless, there is still a lack of understanding in how it relates to convective organization in the observed world. Numerous studies have examined self-aggregation using idealized Cloud Resolving Models (CRMs) and General Circulation Models over the ocean, however very little work has been done on RCE and self-aggregation over land. Idealized models of RCE over ocean have shown that aggregation is sensitive to sea surface temperature (SST), more intense precipitation occurs in aggregated systems, and a variety of feedbacks—such as surface flux, cloud radiative, and upgradient moisture transport— contribute to the maintenance of aggregation, however it is not clear if these results apply over land. Progress in this area could help relate understanding of self-aggregation in idealized simulations to observations. In order to explore the behavior of self-aggregation over land, we use a CRM to simulate idealized RCE over land. In particular, we examine the aggregation of convection and how it compares with aggregation over ocean. Based on previous studies, where a variety of different CRMs exhibit a SST threshold below which self-aggregation does not occur, we hypothesize

Microwave-induced formation of oligomeric amyloid aggregates.

PubMed

Lee, Wonseok; Choi, Yeseong; Lee, Sang Won; Kim, Insu; Lee, Dongtak; Hong, Yoochan; Lee, Gyudo; Yoon, Dae Sung

2018-08-24

Amyloid aggregates have emerged as a significant hallmark of neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Although it has been recently reported that microwave heating induces amyloid aggregation compared with conventional heating methods, the mechanism of amyloid aggregate induction has remained unclear. In this study, we investigated the formation of oligomeric amyloid aggregates (OAAs) by microwave irradiation at microscale volumes of solution. Microwave irradiation of protein monomer solution triggered rapid formation of OAAs within 7 min. We characterized the formation of OAAs using atomic force microscopy, thioflavin T fluorescent assay and circular dichroism. In the microwave system, we also investigated the inhibitory effect on the formation of amyloid aggregates by L-ascorbic acid as well as enhanced amyloid aggregation by silver nanomaterials such as nanoparticles and nanowires. We believe that microwave technology has the potential to facilitate the study of amyloid aggregation in the presence of chemical agents or nanomaterials.

pH-responsive modulation of insulin aggregation and structural transformation of the aggregates.

PubMed

Smirnova, Ekaterina; Safenkova, Irina; Stein-Margolina, Vita; Shubin, Vladimir; Polshakov, Vladimir; Gurvits, Bella

2015-02-01

Over the past two decades, much information has appeared on electrostatically driven molecular mechanisms of protein self-assembly and formation of aggregates of different morphology, varying from soluble amorphous structures to highly-ordered amyloid-like fibrils. Protein aggregation represents a special tool in biomedicine and biotechnology to produce biological materials for a wide range of applications. This has awakened interest in identification of pH-triggered regulators of transformation of aggregation-prone proteins into structures of higher order. The objective of the present study is to elucidate the effects of low-molecular-weight biogenic agents on aggregation and formation of supramolecular structures of human recombinant insulin, as a model therapeutic protein. Using dynamic light scattering, turbidimetry, circular dichroism, fluorescence spectroscopy, atomic force microscopy, transmission electron microscopy, and nuclear magnetic resonance, we have demonstrated that the amino acid l-arginine (Arg) has the striking potential to influence insulin aggregation propensity. It was shown that modification of the net charge of insulin induced by changes in the pH level of the incubation medium results in dramatic changes in the interaction of the protein with Arg. We have revealed the dual effects of Arg, highly dependent on the pH level of the solution - suppression or acceleration of the aggregation of insulin at pH 7.0 or 8.0, respectively. These effects can be regulated by manipulating the pH of the environment. The results of this study may be of interest for development of appropriate drug formulations and for the more general insight into the functioning of insulin in living systems, as the protein is known to release by exocytosis from pancreatic beta cells in a pH-dependent manner. Copyright © 2014 Elsevier B.V. and Société française de biochimie et biologie Moléculaire (SFBBM). All rights reserved.

Bacterial prostatitis.

PubMed

Gill, Bradley C; Shoskes, Daniel A

2016-02-01

The review provides the infectious disease community with a urologic perspective on bacterial prostatitis. Specifically, the article briefly reviews the categorization of prostatitis by type and provides a distillation of new findings published on bacterial prostatitis over the past year. It also highlights key points from the established literature. Cross-sectional prostate imaging is becoming more common and may lead to more incidental diagnoses of acute bacterial prostatitis. As drug resistance remains problematic in this condition, the reemergence of older antibiotics such as fosfomycin, has proven beneficial. With regard to chronic bacterial prostatitis, no clear clinical risk factors emerged in a large epidemiological study. However, bacterial biofilm formation has been associated with more severe cases. Surgery has a limited role in bacterial prostatitis and should be reserved for draining of a prostatic abscess or the removal of infected prostatic stones. Prostatitis remains a common and bothersome clinical condition. Antibiotic therapy remains the basis of treatment for both acute and chronic bacterial prostatitis. Further research into improving prostatitis treatment is indicated.

Bacterial Sialidase

NASA Technical Reports Server (NTRS)

2004-01-01

Data shows that elevated sialidase in bacterial vaginosis patients correlates to premature births in women. Bacterial sialidase also plays a significant role in the unusual colonization of Pseudomonas aeruginosa in cystic fibrosis patients. Crystals of Salmonella sialidase have been reproduced and are used for studying the inhibitor-enzyme complexes. These inhibitors may also be used to inhibit a trans-sialidase of Trypanosome cruzi, a very similar enzyme to bacterial sialidase, therefore preventing T. cruzi infection, the causitive agent of Chagas' disease. The Center for Macromolecular Crystallography suggests that inhibitors of bacterial sialidases can be used as prophylactic drugs to prevent bacterial infections in these critical cases.

Cholesterol impairment contributes to neuroserpin aggregation

NASA Astrophysics Data System (ADS)

Giampietro, Costanza; Lionetti, Maria Chiara; Costantini, Giulio; Mutti, Federico; Zapperi, Stefano; La Porta, Caterina A. M.

2017-03-01

Intraneural accumulation of misfolded proteins is a common feature of several neurodegenerative pathologies including Alzheimer’s and Parkinson’s diseases, and Familial Encephalopathy with Neuroserpin Inclusion Bodies (FENIB). FENIB is a rare disease due to a point mutation in neuroserpin which accelerates protein aggregation in the endoplasmic reticulum (ER). Here we show that cholesterol depletion induced either by prolonged exposure to statins or by inhibiting the sterol reg-ulatory binding-element protein (SREBP) pathway also enhances aggregation of neuroserpin proteins. These findings can be explained considering a computational model of protein aggregation under non-equilibrium conditions, where a decrease in the rate of protein clearance improves aggregation. Decreasing cholesterol in cell membranes affects their biophysical properties, including their ability to form the vesicles needed for protein clearance, as we illustrate by a simple mathematical model. Taken together, these results suggest that cholesterol reduction induces neuroserpin aggregation, even in absence of specific neuroserpin mutations. The new mechanism we uncover could be relevant also for other neurodegenerative diseases associated with protein aggregation.

The Influence of Organic Material and Temperature on the Burial Tolerance of the Blue Mussel, Mytilus edulis: Considerations for the Management of Marine Aggregate Dredging

PubMed Central

Cottrell, Richard S.; Black, Kenny D.; Hutchison, Zoë L.; Last, Kim S.

2016-01-01

Rationale and Experimental Approach Aggregate dredging is a growing source of anthropogenic disturbance in coastal UK waters and has the potential to impact marine systems through the smothering of benthic fauna with organically loaded screening discards. This study investigates the tolerance of the blue mussel, Mytilus edulis to such episodic smothering events using a multi-factorial design, including organic matter concentration, temperature, sediment fraction size and duration of burial as important predictor variables. Results and Discussion Mussel mortality was significantly higher in organically loaded burials when compared to control sediments after just 2 days. Particularly, M. edulis specimens under burial in fine sediment with high (1%) concentrations of organic matter experienced a significantly higher mortality rate (p<0.01) than those under coarse control aggregates. Additionally, mussels exposed to the summer maximum temperature treatment (20°C) exhibited significantly increased mortality (p<0.01) compared to those in the ambient treatment group (15°C). Total Oxygen Uptake rates of experimental aggregates were greatest (112.7 mmol m-2 day-1) with 1% organic loadings in coarse sediment at 20°C. Elevated oxygen flux rates in porous coarse sediments are likely to be a function of increased vertical migration of anaerobically liberated sulphides to the sediment-water interface. However, survival of M. edulis under bacterial mats of Beggiatoa spp. indicates the species’ resilience to sulphides and so we propose that the presence of reactive organic matter within the burial medium may facilitate bacterial growth and increase mortality through pathogenic infection. This may be exacerbated under the stable interstitial conditions in fine sediment and increased bacterial metabolism under high temperatures. Furthermore, increased temperature may impose metabolic demands upon the mussel that cannot be met during burial-induced anaerobiosis. Summary Lack of

Influence of aqueous media properties on aggregation and solubility of four structurally related meso-porphyrin photosensitizers evaluated by spectrophotometric measurements.

PubMed

Sobczyński, J; Tønnesen, H H; Kristensen, S

2013-02-01

Porphyrin photosensitizers tend to aggregate in aqueous solutions even in the micromolar concentration range. This is a challenge during formulation of e.g., parenteral preparations for photodynamic cancer therapy, or preparations for local or topical administration in antimicrobial photodynamic therapy. Monomerization is essential to achieve biocompatible drug formulations of high bioavailability and physiological response (i.e., photoreactivity) and low toxicity. The aggregation and solubilization of four structurally related meso-tetraphenyl porphyrin photosensitizers with nonionic (4-hydroxy), anionic (4-sulphonate; 4-carboxy) and cationic (4-trimethylanilinium) substituents were evaluated in various vehicles by use of UV-Vis spectroscopy. Substituents, overall charge and charge distribution influenced the pKa-values and interaction of the porphyrins with different solvents, excipients and impurities. Modification of medium polarity and solubilization by the nonionic surfactant Tween 80 adjusted the acid-base equilibria and increased the solubility by reduction of porphyrin aggregation. The selected porphyrins were sensitive towards ionic strength, temperature and inorganic impurities to various extents. The results will be further used during development of parenteral and topical formulations of porphyrin photosensitizers for use in photodynamic therapy of cancer and bacterial infections.

Mechanical properties of recycled concrete with demolished waste concrete aggregate and clay brick aggregate

NASA Astrophysics Data System (ADS)

Zheng, Chaocan; Lou, Cong; Du, Geng; Li, Xiaozhen; Liu, Zhiwu; Li, Liqin

2018-06-01

This paper presents an experimental investigation on the effect of the replacement of natural coarse aggregate (NCA) with either recycled concrete aggregate (RCA) or recycled clay brick aggregate (RBA) on the compressive strengths of the hardened concrete. Two grades (C25 and C50) of concrete were investigated, which were achieved by using different water-to-cement ratios. In each grade concrete five different replacement rates, 0%, 25%, 50%, 75% and 100% were considered. In order to improve the performance of the recycled aggregates in the concrete mixes, the RCA and RBA were carefully sieved by using the optimal degradation. In this way the largest reduction in the 28-day compressive strength was found to be only 7.2% and 9.6% for C25 and C50 recycled concrete when the NCA was replaced 100% by RCA, and 11% and 13% for C25 and C50 recycled concrete when the NCA was replaced 100% by RBA. In general, the concrete with RCA has better performance than the concrete with RBA. The comparison of the present experimental results with those reported in literature for hardened concrete with either RCA or RBA demonstrates the effectiveness in improving the compressive strength by using the optimal gradation of recycled aggregates.

Stimulative effect of the fungal biocontrol agent Fusarium oxysporum f.sp. Striga on abundance of nitrifying prokaryotes in a maize rhizosphere

NASA Astrophysics Data System (ADS)

Musyoki, Mary; Enowashu, Esther; Zimmermann, Judith; Muema, Esther; Wainright, Henry; Vanlauwe, Bernard; Cadisch, Georg; Rasche, Frank

2014-05-01

The integration of resistant crop varieties and Fusarium oxysporum f.sp. strigae (Foxy-2) strains as biological control agent (BCA) has shown to be an effective control of the weed Striga hermonthica which is parasitic to several cereals (e.g., maize) cultivated in Sub-Saharan Africa. Most studies have examined the efficacy of the BCA and its interactions with host crops, while overlooking the interplay among key microorganisms in the soil nitrogen (N) cycle. Hence, we postulated that both Foxy-2 and Striga pose threats to the indigenous plant root-associated microbial communities involved in N cycling through direct or indirect competition for nutrients and that the application of high quality organic residues would compensate these effects. The primary objective of this study was thus to assess the potential impact of Foxy-2 on indigenous nitrifying prokaryotes in maize rhizosphere cultivated on two distinct soils (sandy Ferric Alisol versus clayey Humic Nitisol) obtained from Machanga and Embu, respectively, in central Kenya. These soils were treated with or without Foxy-2 and Striga; and in combination with high quality (i.e. CN ratio; 13, lignins, 8.9 % and polyphenols, 1.7 %) organic residues (i.e., Tithonia diversifolia) as N source. Using quantitative polymerase chain reaction (qPCR), we followed at three pre-defined sampling dates (14, 28 and 42 days after planting) the responses of ammonia-oxidizing archaea (AOA) and bacteria (AOB), total bacteria and archaea in four treatments of a rhizobox experiment: (i) Foxy-2 plus Striga (F+S), (ii) Striga only (C+S), (iii) Foxy-2 plus Striga plus Tithonia diversifolia residues (F+S+T), and (iv) a non-treated control (C). Overall, the treatment effects on soil microbial populations were, in comparison to the clayey Embu soil, more pronounced in the sandy Machanga soil. Contrary to our expectations, we observed a distinct stimulative, but no resource competition effect of Foxy-2 on the abundance of AOA, as well as

Bacterial Standing Stock, Activity, and Carbon Production during Formation and Growth of Sea Ice in the Weddell Sea, Antarctica.

PubMed

Grossmann, S; Dieckmann, G S

1994-08-01

Bacterial response to formation and growth of sea ice was investigated during autumn in the northeastern Weddell Sea. Changes in standing stock, activity, and carbon production of bacteria were determined in successive stages of ice development. During initial ice formation, concentrations of bacterial cells, in the order of 1 x 10 to 3 x 10 liter, were not enhanced within the ice matrix. This suggests that physical enrichment of bacteria by ice crystals is not effective. Due to low concentrations of phytoplankton in the water column during freezing, incorporation of bacteria into newly formed ice via attachment to algal cells or aggregates was not recorded in this study. As soon as the ice had formed, the general metabolic activity of bacterial populations was strongly suppressed. Furthermore, the ratio of [H]leucine incorporation into proteins to [H]thymidine incorporation into DNA changed during ice growth. In thick pack ice, bacterial activity recovered and growth rates up to 0.6 day indicated actively dividing populations. However, biomass-specific utilization of organic compounds remained lower than in open water. Bacterial concentrations of up to 2.8 x 10 cells liter along with considerably enlarged cell volumes accumulated within thick pack ice, suggesting reduced mortality rates of bacteria within the small brine pores. In the course of ice development, bacterial carbon production increased from about 0.01 to 0.4 mug of C liter h. In thick ice, bacterial secondary production exceeded primary production of microalgae.

Role of Streptococcus sanguinis sortase A in bacterial colonization.

PubMed

Yamaguchi, Masaya; Terao, Yutaka; Ogawa, Taiji; Takahashi, Toshihito; Hamada, Shigeyuki; Kawabata, Shigetada

2006-10-01

Streptococcus sanguinis, a normal inhabitant of the human oral cavity, has low cariogenicity, though colonization on tooth surfaces by this bacterium initiates aggregation by other oral bacteria and maturation of dental plaque. Additionally, S. sanguinis is frequently isolated from infective endocarditis patients. We investigated the functions of sortase A (SrtA), which cleaves LPXTG-containing proteins and anchors them to the bacterial cell wall, as a possible virulence factor of S. sanguinis. We identified the srtA gene of S. sanguinis by searching a homologous gene of Streptococcus mutans in genome databases. Next, we constructed an srtA-deficient mutant strain of S. sanguinis by insertional inactivation and compared it to the wild type strain. In the case of the mutant strain, some surface proteins could not anchor to the cell wall and were partially released into the culture supernatant. Furthermore, adherence to saliva-coated hydroxyapatite beads and polystyrene plates, as well as adherence to and invasion of human epithelial cells were reduced significantly in the srtA-deficient strain when compared to the wild type. In addition, antiopsonization levels and bacterial survival of the srtA-deficient mutant were decreased in human whole blood. This is the first known study to report that SrtA contributes to antiopsonization in streptococci. Our results suggest that SrtA anchors surface adhesins as well as some proteins that function as antiopsonic molecules as a means of evading the human immune system. Furthermore, they demonstrate that SrtA of S. sanguinis plays important roles in bacterial colonization.

Mining databases for protein aggregation: a review.

PubMed

Tsiolaki, Paraskevi L; Nastou, Katerina C; Hamodrakas, Stavros J; Iconomidou, Vassiliki A

2017-09-01

Protein aggregation is an active area of research in recent decades, since it is the most common and troubling indication of protein instability. Understanding the mechanisms governing protein aggregation and amyloidogenesis is a key component to the aetiology and pathogenesis of many devastating disorders, including Alzheimer's disease or type 2 diabetes. Protein aggregation data are currently found "scattered" in an increasing number of repositories, since advances in computational biology greatly influence this field of research. This review exploits the various resources of aggregation data and attempts to distinguish and analyze the biological knowledge they contain, by introducing protein-based, fragment-based and disease-based repositories, related to aggregation. In order to gain a broad overview of the available repositories, a novel comprehensive network maps and visualizes the current association between aggregation databases and other important databases and/or tools and discusses the beneficial role of community annotation. The need for unification of aggregation databases in a common platform is also addressed.

Analysis of the cellulose synthase operon genes, bcsA, bcsB, and bcsC in Cronobacter species: Prevalence among species and their roles in biofilm formation and cell-cell aggregation.

PubMed

Hu, Lan; Grim, Christopher J; Franco, Augusto A; Jarvis, Karen G; Sathyamoorthy, Vengopal; Kothary, Mahendra H; McCardell, Barbara A; Tall, Ben D

2015-12-01

Cronobacter species are emerging food-borne pathogens that cause severe sepsis, meningitis, and necrotizing entercolitis in neonates and infants. Bacterial pathogens such as Escherichia coli and Salmonella species produce extracellular cellulose which has been shown to be involved in rugosity, biofilm formation, and host colonization. In this study the distribution and prevalence of cellulose synthase operon genes (bcsABZC) were determined by polymerase chain reaction (PCR) analysis in 231 Cronobacter strains isolated from clinical, food, environmental, and unknown sources. Furthermore, bcsA and bcsB isogenic mutants were constructed in Cronobacter sakazakii BAA894 to determine their roles. In calcofluor binding assays bcsA and bcsB mutants did not produce cellulose, and their colonial morphotypes were different to that of the parent strain. Biofilm formation and bacterial cell-cell aggregation were significantly reduced in bcsA and bcsB mutants compared to the parental strain. bcsA or bcsAB PCR-negative strains of C. sakazakii did not bind calcofluor, and produced less biofilm and cell-cell aggregation compared to strains possessing bcsAB genes. These data indicated that Cronobacter bcsABZC were present in all clinical isolates and most of food and environmental isolates. bcsA and bcsB genes of Cronobacter were necessary to produce cellulose, and were involved in biofilm formation and cell-cell aggregation. Published by Elsevier Ltd.

Aggregate Load Controllers and Associated Methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chassin, David P.

Aggregate load controllers and associated methods are described. According to one aspect, a method of operating an aggregate load controller includes using an aggregate load controller having an initial state, applying a stimulus to a plurality of thermostatic controllers which are configured to control a plurality of respective thermostatic loads which receive electrical energy from an electrical utility to operate in a plurality of different operational modes, accessing data regarding a response of the thermostatic loads as a result of the applied stimulus, using the data regarding the response, determining a value of at least one design parameter of themore » aggregate load controller, and using the determined value of the at least one design parameter, configuring the aggregate load controller to control amounts of the electrical energy which are utilized by the thermostatic loads.« less

Aggregation of flexible polyelectrolytes: Phase diagram and dynamics.

PubMed

Tom, Anvy Moly; Rajesh, R; Vemparala, Satyavani

2017-10-14

Similarly charged polymers in solution, known as polyelectrolytes, are known to form aggregated structures in the presence of oppositely charged counterions. Understanding the dependence of the equilibrium phases and the dynamics of the process of aggregation on parameters such as backbone flexibility and charge density of such polymers is crucial for insights into various biological processes which involve biological polyelectrolytes such as protein, DNA, etc. Here, we use large-scale coarse-grained molecular dynamics simulations to obtain the phase diagram of the aggregated structures of flexible charged polymers and characterize the morphology of the aggregates as well as the aggregation dynamics, in the presence of trivalent counterions. Three different phases are observed depending on the charge density: no aggregation, a finite bundle phase where multiple small aggregates coexist with a large aggregate and a fully phase separated phase. We show that the flexibility of the polymer backbone causes strong entanglement between charged polymers leading to additional time scales in the aggregation process. Such slowing down of the aggregation dynamics results in the exponent, characterizing the power law decay of the number of aggregates with time, to be dependent on the charge density of the polymers. These results are contrary to those obtained for rigid polyelectrolytes, emphasizing the role of backbone flexibility.

Dispersion of ferrofluid aggregates in steady flows

NASA Astrophysics Data System (ADS)

Williams, Alicia M.; Vlachos, Pavlos P.

2011-12-01

Using focused shadowgraphs, we investigate steady flows of a magnetically non-susceptible fluid interacting with ferrofluid aggregates comprised of superparamagnetic nanoparticles. The ferrofluid aggregate is retained at a specific site within the flow channel using two different applied magnetic fields. The bulk flow induces shear stresses on the aggregate, which give rise to the development of interfacial disturbances, leading to Kelvin-Helmholtz (K-H) instabilities and shedding of ferrofluid structures. Herein, the effects of bulk Reynolds number, ranging from 100 to 1000, and maximum applied magnetic fields of 1.2 × 105 and 2.4 × 105 A/m are investigated in the context of their impact on dispersion or removal of material from the core aggregate. The aggregate interaction with steady bulk flow reveals three regimes of aggregate dynamics over the span of Reynolds numbers studied: stable, transitional, and shedding. The first regime is characterized by slight aggregate stretching for low Reynolds numbers, with full aggregate retention. As the Reynolds number increases, the aggregate is in-transition between stable and shedding states. This second regime is characterized by significant initial stretching that gives way to small amplitude Kelvin-Helmholtz waves. Higher Reynolds numbers result in ferrofluid shedding, with Strouhal numbers initially between 0.2 and 0.3, wherein large vortical structures are shed from the main aggregate accompanied by precipitous decay of the accumulated ferrofluid aggregate. These behaviors are apparent for both magnetic field strengths, although the transitional Reynolds numbers are different between the cases, as are the characteristic shedding frequencies relative to the same Reynolds number. In the final step of this study, relevant parameters were extracted from the time series dispersion data to comprehensively quantify aggregate mechanics. The aggregate half-life is found to decrease as a function of the Reynolds number

Mechanisms of the priming effect of low doses of lipopoly-saccharides on leukocyte-dependent platelet aggregation in whole blood.

PubMed

Montrucchio, Giuseppe; Bosco, Ornella; Del Sorbo, Lorenzo; Fascio Pecetto, Paolo; Lupia, Enrico; Goffi, Alberto; Omedè, Paola; Emanuelli, Giorgio; Camussi, Giovanni

2003-11-01

Several studies focused on the ability of bacterial lipopolysac-charides (LPS) in triggering platelet and/or leukocyte activation. The aim of this study was to investigate the molecular mechanisms involved in the aggregation of platelets and in their interaction with leukocytes in whole blood after stimulation with low doses of LPS. LPS did not directly induce platelet aggregation in whole blood, but they primed the aggregation of platelets induced by epinephrine, adenosine diphosphate and arachidonic acid. As shown by cytofluorimetry, platelets neither bind FITC-LPS, nor express the LPS-receptors CD14 and toll-like receptor 4 (TLR4). On the contrary, LPS primed monocytes and to a lesser extent polymorphonuclear neutrophils to adhere to platelets. Both platelet-leukocyte interaction and platelet aggregation in whole blood were inhibited by blockade of CD14 and TLR4. Moreover, the interaction between platelets and leukocytes was inhibited by P-selectin, and by blockade of PAF and reactive oxygen species, suggesting a role of P-selectin and of leukocyte-derived mediators. In conclusion, these results elucidate the mechanisms leading to platelet activation and interaction with leukocytes triggered by LPS. They suggest that the activation of platelets by LPS is mainly dependent on leukocytes and especially monocytes as a result of CD14 and TLR4 engagement. Moreover, we found that leukocyte-platelet interaction was triggered by the synthesis of PAF and the generation of oxygen radicals that induced upregulation of surface expression of P-selectin.

31 CFR 1024.313 - Aggregation.

Code of Federal Regulations, 2011 CFR

2011-07-01

... ENFORCEMENT NETWORK, DEPARTMENT OF THE TREASURY RULES FOR MUTUAL FUNDS Reports Required To Be Made By Mutual Funds § 1024.313 Aggregation. Refer to § 1010.313 of this chapter for reports of transactions in currency aggregation requirements for mutual funds. ...

Methods of predicting aggregate voids : [technical summary].

DOT National Transportation Integrated Search

2013-03-01

Percent voids in combined aggregates vary significantly. Simplified methods of predicting aggregate voids were studied to determine the feasibility of a range of gradations using aggregates available in Kansas. : The 0.45 Power Curve Void Prediction ...

Self-aggregation and coaggregation of the p53 core fragment with its aggregation gatekeeper variant.

PubMed

Lei, Jiangtao; Qi, Ruxi; Wei, Guanghong; Nussinov, Ruth; Ma, Buyong

2016-03-21

Recent studies suggested that p53 aggregation can lead to loss-of-function (LoF), dominant-negative (DN) and gain-of-function (GoF) effects, with adverse cancer consequences. The p53 aggregation-nucleating (251)ILTIITL(257) fragment is a key segment in wild-type p53 aggregation; however, an I254R mutation can prevent it. It was suggested that self-assembly of wild-type p53 and its cross-interaction with mutants differ from the classical amyloid nucleation-growth mechanism. Here, using replica exchange molecular dynamics (REMD) simulations, we studied the cross-interactions of this p53 core fragment and its aggregation rescue I254R mutant. We found that the core fragment displays strong aggregation propensity, whereas the gatekeeper I254R mutant tends to be disordered, consistent with experiments. Our cross-interaction results reveal that the wild-type p53 fragment promotes β-sheet formation of the I254R mutant by shifting the disordered mutant peptides into aggregating states. As a result, the system has similar oligomeric structures, inter-peptide interactions and free energy landscape as the wild type fragment does, revealing a prion-like process. We also found that in the cross-interaction system, the wild-type species has higher tendency to interact with the mutant than with itself. This phenomenon illustrates synergistic effects between the p53 (251)ILTIITL(257) fragment and the mutant resembling prion cross-species propagation, cautioning against exploiting it in drug discovery.

Small file aggregation in a parallel computing system

DOEpatents

Faibish, Sorin; Bent, John M.; Tzelnic, Percy; Grider, Gary; Zhang, Jingwang

2014-09-02

Techniques are provided for small file aggregation in a parallel computing system. An exemplary method for storing a plurality of files generated by a plurality of processes in a parallel computing system comprises aggregating the plurality of files into a single aggregated file; and generating metadata for the single aggregated file. The metadata comprises an offset and a length of each of the plurality of files in the single aggregated file. The metadata can be used to unpack one or more of the files from the single aggregated file.

Active protein aggregates induced by terminally attached self-assembling peptide ELK16 in Escherichia coli

PubMed Central

2011-01-01

Background In recent years, it has been gradually realized that bacterial inclusion bodies (IBs) could be biologically active. In particular, several proteins including green fluorescent protein, β-galactosidase, β-lactamase, alkaline phosphatase, D-amino acid oxidase, polyphosphate kinase 3, maltodextrin phosphorylase, and sialic acid aldolase have been successfully produced as active IBs when fused to an appropriate partner such as the foot-and-mouth disease virus capsid protein VP1, or the human β-amyloid peptide Aβ42(F19D). As active IBs may have many attractive advantages in enzyme production and industrial applications, it is of considerable interest to explore them further. Results In this paper, we report that an ionic self-assembling peptide ELK16 (LELELKLK)2 was able to effectively induce the formation of cytoplasmic inclusion bodies in Escherichia coli (E. coli) when attached to the carboxyl termini of four model proteins including lipase A, amadoriase II, β-xylosidase, and green fluorescent protein. These aggregates had a general appearance similar to the usually reported cytoplasmic inclusion bodies (IBs) under transmission electron microscopy or fluorescence confocal microscopy. Except for lipase A-ELK16 fusion, the three other fusion protein aggregates retained comparable specific activities with the native counterparts. Conformational analyses by Fourier transform infrared spectroscopy revealed the existence of newly formed antiparallel beta-sheet structures in these ELK16 peptide-induced inclusion bodies, which is consistent with the reported assembly of the ELK16 peptide. Conclusions This has been the first report where a terminally attached self-assembling β peptide ELK16 can promote the formation of active inclusion bodies or active protein aggregates in E. coli. It has the potential to render E. coli and other recombinant hosts more efficient as microbial cell factories for protein production. Our observation might also provide hints for

Island size distribution with hindered aggregation

NASA Astrophysics Data System (ADS)

González, Diego Luis; Camargo, Manuel; Sánchez, Julián A.

2018-05-01

We study the effect of hindered aggregation on the island formation processes for a one-dimensional model of epitaxial growth with arbitrary nucleus size i . In the proposed model, the attachment of monomers to islands is hindered by an aggregation barrier, ɛa, which decreases the hopping rate of monomers to the islands. As ɛa increases, the system exhibits a crossover between two different regimes; namely, from diffusion-limited aggregation to attachment-limited aggregation. The island size distribution, P (s ) , is calculated for different values of ɛa by a self-consistent approach involving the nucleation and aggregation capture kernels. The results given by the analytical model are compared with those from kinetic Monte Carlo simulations, finding a close agreement between both sets of data for all considered values of i and ɛa. As the aggregation barrier increases, the spatial effect of fluctuations on the density of monomers can be neglected and P (s ) smoothly approximates to the limit distribution P (s ) =δs ,i +1 . In the crossover regime the system features a complex and rich behavior, which can be explained in terms of the characteristic timescales of different microscopic processes.

Mechanical Dissociation of Platelet Aggregates in Blood Stream

NASA Astrophysics Data System (ADS)

Hoore, Masoud; Fedosov, Dmitry A.; Gompper, Gerhard; Complex; Biological Fluids Group Team

2017-11-01

von Willebrand factor (VWF) and platelet aggregation is a key phenomenon in blood clotting. These aggregates form critically in high shear rates and dissolve reversibly in low shear rates. The emergence of a critical shear rate, beyond which aggregates form and below which they dissolve, has an interesting impact on aggregation in blood flow. As red blood cells (RBCs) migrate to the center of the vessel in blood flow, a RBC free layer (RBC-FL) is left close to the walls into which the platelets and VWFs are pushed back from the bulk flow. This margination process provides maximal VWF-platelet aggregation probability in the RBC-FL. Using mesoscale hydrodynamic simulations of aggregate dynamics in blood flow, it is shown that the aggregates form and grow in RBC-FL wherein shear rate is high for VWF stretching. By growing, the aggregates penetrate to the bulk flow and get under order of magnitude lower shear rates. Consequently, they dissolve and get back into the RBC-FL. This mechanical limitation for aggregates prohibits undesired thrombosis and vessel blockage by aggregates, while letting the VWFs and platelets to aggregate close to the walls where they are actually needed. The support by the DFG Research Unit FOR 1543 SHENC and CPU time Grant by the Julich Supercomputing Center are acknowledged.

Classification and Characterization of Therapeutic Antibody Aggregates

PubMed Central

Joubert, Marisa K.; Luo, Quanzhou; Nashed-Samuel, Yasser; Wypych, Jette; Narhi, Linda O.

2011-01-01

A host of diverse stress techniques was applied to a monoclonal antibody (IgG2) to yield protein particles with varying attributes and morphologies. Aggregated solutions were evaluated for percent aggregation, particle counts, size distribution, morphology, changes in secondary and tertiary structure, surface hydrophobicity, metal content, and reversibility. Chemical modifications were also identified in a separate report (Luo, Q., Joubert, M. K., Stevenson, R., Narhi, L. O., and Wypych, J. (2011) J. Biol. Chem. 286, 25134–25144). Aggregates were categorized into seven discrete classes, based on the traits described. Several additional molecules (from the IgG1 and IgG2 subtypes as well as intravenous IgG) were stressed and found to be defined with the same classification system. The mechanism of protein aggregation and the type of aggregate formed depends on the nature of the stress applied. Different IgG molecules appear to aggregate by a similar mechanism under the same applied stress. Aggregates created by harsh mechanical stress showed the largest number of subvisible particles, and the class generated by thermal stress displayed the largest number of visible particles. Most classes showed a disruption of the higher order structure, with the degree of disorder depending on the stress process. Particles in all classes (except thermal stress) were at least partially reversible upon dilution in pH 5 buffer. High copper content was detected in isolated metal-catalyzed aggregates, a stress previously shown to produce immunogenic aggregates. In conclusion, protein aggregates can be a very heterogeneous population, whose qualities are the result of the type of stress that was experienced. PMID:21454532

Learning about individuals' health from aggregate data.

PubMed

Colbaugh, Rich; Glass, Kristin

2017-07-01

There is growing awareness that user-generated social media content contains valuable health-related information and is more convenient to collect than typical health data. For example, Twitter has been employed to predict aggregate-level outcomes, such as regional rates of diabetes and child poverty, and to identify individual cases of depression and food poisoning. Models which make aggregate-level inferences can be induced from aggregate data, and consequently are straightforward to build. In contrast, learning models that produce individual-level (IL) predictions, which are more informative, usually requires a large number of difficult-to-acquire labeled IL examples. This paper presents a new machine learning method which achieves the best of both worlds, enabling IL models to be learned from aggregate labels. The algorithm makes predictions by combining unsupervised feature extraction, aggregate-based modeling, and optimal integration of aggregate-level and IL information. Two case studies illustrate how to learn health-relevant IL prediction models using only aggregate labels, and show that these models perform as well as state-of-the-art models trained on hundreds or thousands of labeled individuals.

Efficient clustering aggregation based on data fragments.

PubMed

Wu, Ou; Hu, Weiming; Maybank, Stephen J; Zhu, Mingliang; Li, Bing

2012-06-01

Clustering aggregation, known as clustering ensembles, has emerged as a powerful technique for combining different clustering results to obtain a single better clustering. Existing clustering aggregation algorithms are applied directly to data points, in what is referred to as the point-based approach. The algorithms are inefficient if the number of data points is large. We define an efficient approach for clustering aggregation based on data fragments. In this fragment-based approach, a data fragment is any subset of the data that is not split by any of the clustering results. To establish the theoretical bases of the proposed approach, we prove that clustering aggregation can be performed directly on data fragments under two widely used goodness measures for clustering aggregation taken from the literature. Three new clustering aggregation algorithms are described. The experimental results obtained using several public data sets show that the new algorithms have lower computational complexity than three well-known existing point-based clustering aggregation algorithms (Agglomerative, Furthest, and LocalSearch); nevertheless, the new algorithms do not sacrifice the accuracy.

Aggregate-mediated charge transport in ionomeric electrolytes

NASA Astrophysics Data System (ADS)

Lu, Keran; Maranas, Janna; Milner, Scott

Polymers such PEO can conduct ions, and have been studied as possible replacements for organic liquid electrolytes in rechargeable metal-ion batteries. More generally, fast room-temperature ionic conduction has been reported for a variety of materials, from liquids to crystalline solids. Unfortunately, polymer electrolytes generally have limited conductivity; these polymers are too viscous to have fast ion diffusion like liquids, and too unstructured to promote cooperative transport like crystalline solids. Ionomers are polymer electrolytes in which ionic groups are covalently bound to the polymer backbone, neutralized by free counterions. These materials also conduct ions, and can exhibit strong ionic aggregation. Using coarse-grained molecular dynamics, we explore the forces driving ionic aggregation, and describe the role ion aggregates have in mediating charge transport. The aggregates are string-like such that ions typically have two neighbors. We find ion aggregates self-assemble like worm-like micelles. Excess charge, or free ions, occasionally coordinate with aggregates and are transported along the chain in a Grotthuss-like mechanism. We propose that controlling ionomer aggregate structure through materials design can enhance cooperative ion transport.

Evaluation of ASR potential in Wyoming aggregates.

DOT National Transportation Integrated Search

2013-10-01

A comprehensive study was performed to evaluate the ASR reactivity of eight Wyoming aggregates. State-of-the-art and standardized test : methods were performed and results were used to evaluate these aggregate sources. Of the eight aggregates: four a...

Coupling of aggregation and immunogenicity in biotherapeutics: T- and B-cell immune epitopes may contain aggregation-prone regions.

PubMed

Kumar, Sandeep; Singh, Satish K; Wang, Xiaoling; Rup, Bonita; Gill, Davinder

2011-05-01

Biotherapeutics, including recombinant or plasma-derived human proteins and antibody-based molecules, have emerged as an important class of pharmaceuticals. Aggregation and immunogenicity are among the major bottlenecks during discovery and development of biotherapeutics. Computational tools that can predict aggregation prone regions as well as T- and B-cell immune epitopes from protein sequence and structure have become available recently. Here, we describe a potential coupling between aggregation and immunogenicity: T-cell and B-cell immune epitopes in therapeutic proteins may contain aggregation-prone regions. The details of biological mechanisms behind this observation remain to be understood. However, our observation opens up an exciting potential for rational design of de-immunized novel, as well as follow on biotherapeutics with reduced aggregation propensity.

31 CFR 1026.313 - Aggregation.

Code of Federal Regulations, 2011 CFR

2011-07-01

... IN COMMODITIES Reports Required To Be Made by Futures Commission Merchants and Introducing Brokers in Commodities § 1026.313 Aggregation. Refer to § 1010.313 of this chapter for reports of transactions in currency aggregation requirements for futures commission merchants and introducing brokers in commodities...

21 CFR 864.5700 - Automated platelet aggregation system.

Code of Federal Regulations, 2011 CFR

2011-04-01

... addition of an aggregating reagent to a platelet-rich plasma. (b) Classification. Class II (performance... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Automated platelet aggregation system. 864.5700... § 864.5700 Automated platelet aggregation system. (a) Identification. An automated platelet aggregation...

21 CFR 864.5700 - Automated platelet aggregation system.

Code of Federal Regulations, 2014 CFR

2014-04-01

... addition of an aggregating reagent to a platelet-rich plasma. (b) Classification. Class II (performance... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Automated platelet aggregation system. 864.5700... § 864.5700 Automated platelet aggregation system. (a) Identification. An automated platelet aggregation...

21 CFR 864.5700 - Automated platelet aggregation system.

Code of Federal Regulations, 2013 CFR

2013-04-01

... addition of an aggregating reagent to a platelet-rich plasma. (b) Classification. Class II (performance... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Automated platelet aggregation system. 864.5700... § 864.5700 Automated platelet aggregation system. (a) Identification. An automated platelet aggregation...

21 CFR 864.5700 - Automated platelet aggregation system.

Code of Federal Regulations, 2010 CFR

2010-04-01

... addition of an aggregating reagent to a platelet-rich plasma. (b) Classification. Class II (performance... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Automated platelet aggregation system. 864.5700... § 864.5700 Automated platelet aggregation system. (a) Identification. An automated platelet aggregation...

21 CFR 864.5700 - Automated platelet aggregation system.

Code of Federal Regulations, 2012 CFR

2012-04-01

... addition of an aggregating reagent to a platelet-rich plasma. (b) Classification. Class II (performance... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Automated platelet aggregation system. 864.5700... § 864.5700 Automated platelet aggregation system. (a) Identification. An automated platelet aggregation...

Does bathymetry drive coastal whale shark (Rhincodon typus) aggregations?

PubMed Central

Stewart, Bryce D.; McClean, Colin J.; Hancock, James; Rees, Richard

2018-01-01

Background The whale shark (Rhincodon typus) is known to aggregate in a number of coastal locations globally, however what causes these aggregations to form where they do is largely unknown. This study examines whether bathymetry is an important driver of coastal aggregation locations for R. typus through bathymetry’s effect on primary productivity and prey availability. This is a global study taking into account all coastal areas within R. typus’ range. Methods R. typus aggregation locations were identified through an extensive literature review. Global bathymetric data were compared at R. typus aggregation locations and a large random selection of non-aggregation areas. Generalised linear models were used to assess which bathymetric characteristic had the biggest influence on aggregation presence. Results Aggregation sites were significantly shallower than non-aggregation sites and in closer proximity to deep water (the mesopelagic zone) by two orders of magnitude. Slope at aggregation sites was significantly steeper than non-aggregation sites. These three bathymetric variables were shown to have the biggest association with aggregation sites, with up to 88% of deviation explained by the GLMs. Discussion The three key bathymetric characteristics similar at the aggregation sites are known to induce upwelling events, increase primary productivity and consequently attract numerous other filter feeding species. The location of aggregation sites in these key areas can be attributed to this increased prey availability, thought to be the main reason R. typus aggregations occur, extensively outlined in the literature. The proximity of aggregations to shallow areas such as reefs could also be an important factor why whale sharks thermoregulate after deep dives to feed. These findings increase our understanding of whale shark behaviour and may help guide the identification and conservation of further aggregation sites.

Aggregation of recombinant human botulinum protein antigen serotype C in varying solution conditions: implications of conformational stability for aggregation kinetics.

PubMed

Bai, Shujun; Manning, Mark Cornell; Randolph, Theodore W; Carpenter, John F

2011-03-01

Solution conditions greatly affect the aggregation rate of a protein. Elucidating these influences provides insight into the critical factors governing aggregation. In this study, recombinant human botulinum protein antigen serotype C [rBoNTC (H(c))] was employed as a model protein. rBoNTC (H(c)) aggregated irreversibly during incubation at 42°C. The aggregation rate was studied as a function of solution conditions, including varying the pH from 3.5 to 8.0 and with or without 150 mM NaCl, 7.5% (w/v) trehalose, and 0.5 M urea. Some solution conditions retarded rBoNTC (H(c)) aggregation, whereas others accelerated aggregation, particularly acidic pH and addition of NaCl or urea. To better understand the mechanism by which these solution conditions influenced aggregation rates, the structure of rBoNTC (H(c)) was characterized using circular dichroism, fluorescence, and ultraviolet absorbance spectroscopies. Conformational stability was assessed from equilibrium urea-induced unfolding studies and by using differential scanning calorimetry (DSC). The activation energy of the aggregation reaction (E(a)) was estimated from an analysis of the heating-rate dependence of the thermal transition observed during DSC heating scans. Overall, for rBoNTC (H(c)), an inverse correlation was found between conformational stability and aggregation rate, as well as between the kinetic barrier to unfolding (i.e., E(a)) and aggregation rate. Copyright © 2010 Wiley-Liss, Inc.

Evaluating platelet aggregation dynamics from laser speckle fluctuations.

PubMed

Hajjarian, Zeinab; Tshikudi, Diane M; Nadkarni, Seemantini K

2017-07-01

Platelets are key to maintaining hemostasis and impaired platelet aggregation could lead to hemorrhage or thrombosis. We report a new approach that exploits laser speckle intensity fluctuations, emanated from a drop of platelet-rich-plasma (PRP), to profile aggregation. Speckle fluctuation rate is quantified by the speckle intensity autocorrelation, g 2 (t) , from which the aggregate size is deduced. We first apply this approach to evaluate polystyrene bead aggregation, triggered by salt. Next, we assess dose-dependent platelet aggregation and inhibition in human PRP spiked with adenosine diphosphate and clopidogrel. Additional spatio-temporal speckle analyses yield 2-dimensional maps of particle displacements to visualize platelet aggregate foci within minutes and quantify aggregation dynamics. These findings demonstrate the unique opportunity for assessing platelet health within minutes for diagnosing bleeding disorders and monitoring anti-platelet therapies.

Competitive aggregation dynamics using phase wave signals.

PubMed

Sakaguchi, Hidetsugu; Maeyama, Satomi

2014-10-21

Coupled equations of the phase equation and the equation of cell concentration n are proposed for competitive aggregation dynamics of slime mold in two dimensions. Phase waves are used as tactic signals of aggregation in this model. Several aggregation clusters are formed initially, and target patterns appear around the localized aggregation clusters. Owing to the competition among target patterns, the number of the localized aggregation clusters decreases, and finally one dominant localized pattern survives. If the phase equation is replaced with the complex Ginzburg-Landau equation, several spiral patterns appear, and n is localized near the center of the spiral patterns. After the competition among spiral patterns, one dominant spiral survives. Copyright © 2014 Elsevier Ltd. All rights reserved.

Thermal aggregation of glycated bovine serum albumin.

PubMed

Rondeau, Philippe; Navarra, Giovanna; Cacciabaudo, Francesco; Leone, Maurizio; Bourdon, Emmanuel; Militello, Valeria

2010-04-01

Aggregation and glycation processes in proteins have a particular interest in medicine fields and in food technology. Serum albumins are model proteins which are able to self-assembly in aggregates and also sensitive to a non-enzymatic glycation in cases of diabetes. In this work, we firstly reported a study on the glycation and oxidation effects on the structure of bovine serum albumin (BSA). The experimental approach is based on the study of conformational changes of BSA at secondary and tertiary structures by FTIR absorption and fluorescence spectroscopy, respectively. Secondly, we analysed the thermal aggregation process on BSA glycated with different glucose concentrations. Additional information on the aggregation kinetics are obtained by light scattering measurements. The results show that glycation process affects the native structure of BSA. Then, the partial unfolding of the tertiary structure which accompanies the aggregation process is similar both in native and glycated BSA. In particular, the formation of aggregates is progressively inhibited with growing concentration of glucose incubated with BSA. These results bring new insights on how aggregation process is affected by modification of BSA induced by glycation. Copyright 2009 Elsevier B.V. All rights reserved.

Sequence dependent aggregation of peptides and fibril formation

NASA Astrophysics Data System (ADS)

Hung, Nguyen Ba; Le, Duy-Manh; Hoang, Trinh X.

2017-09-01

Deciphering the links between amino acid sequence and amyloid fibril formation is key for understanding protein misfolding diseases. Here we use Monte Carlo simulations to study the aggregation of short peptides in a coarse-grained model with hydrophobic-polar (HP) amino acid sequences and correlated side chain orientations for hydrophobic contacts. A significant heterogeneity is observed in the aggregate structures and in the thermodynamics of aggregation for systems of different HP sequences and different numbers of peptides. Fibril-like ordered aggregates are found for several sequences that contain the common HPH pattern, while other sequences may form helix bundles or disordered aggregates. A wide variation of the aggregation transition temperatures among sequences, even among those of the same hydrophobic fraction, indicates that not all sequences undergo aggregation at a presumable physiological temperature. The transition is found to be the most cooperative for sequences forming fibril-like structures. For a fibril-prone sequence, it is shown that fibril formation follows the nucleation and growth mechanism. Interestingly, a binary mixture of peptides of an aggregation-prone and a non-aggregation-prone sequence shows the association and conversion of the latter to the fibrillar structure. Our study highlights the role of a sequence in selecting fibril-like aggregates and also the impact of a structural template on fibril formation by peptides of unrelated sequences.

Cellular Strategies for Regulating Functional and Nonfunctional Protein Aggregation

PubMed Central

Gsponer, Jörg; Babu, M. Madan

2012-01-01

Summary Growing evidence suggests that aggregation-prone proteins are both harmful and functional for a cell. How do cellular systems balance the detrimental and beneficial effect of protein aggregation? We reveal that aggregation-prone proteins are subject to differential transcriptional, translational, and degradation control compared to nonaggregation-prone proteins, which leads to their decreased synthesis, low abundance, and high turnover. Genetic modulators that enhance the aggregation phenotype are enriched in genes that influence expression homeostasis. Moreover, genes encoding aggregation-prone proteins are more likely to be harmful when overexpressed. The trends are evolutionarily conserved and suggest a strategy whereby cellular mechanisms specifically modulate the availability of aggregation-prone proteins to (1) keep concentrations below the critical ones required for aggregation and (2) shift the equilibrium between the monomeric and oligomeric/aggregate form, as explained by Le Chatelier’s principle. This strategy may prevent formation of undesirable aggregates and keep functional assemblies/aggregates under control. PMID:23168257

Biological framework for soil aggregation: Implications for ecological functions.

NASA Astrophysics Data System (ADS)

Ghezzehei, Teamrat; Or, Dani

2016-04-01

Soil aggregation is heuristically understood as agglomeration of primary particles bound together by biotic and abiotic cementing agents. The organization of aggregates is believed to be hierarchical in nature; whereby primary particles bond together to form secondary particles and subsequently merge to form larger aggregates. Soil aggregates are not permanent structures, they continuously change in response to internal and external forces and other drivers, including moisture, capillary pressure, temperature, biological activity, and human disturbances. Soil aggregation processes and the resulting functionality span multiple spatial and temporal scales. The intertwined biological and physical nature of soil aggregation, and the time scales involved precluded a universally applicable and quantifiable framework for characterizing the nature and function of soil aggregation. We introduce a biophysical framework of soil aggregation that considers the various modes and factors of the genesis, maturation and degradation of soil aggregates including wetting/drying cycles, soil mechanical processes, biological activity and the nature of primary soil particles. The framework attempts to disentangle mechanical (compaction and soil fragmentation) from in-situ biophysical aggregation and provides a consistent description of aggregate size, hierarchical organization, and life time. It also enables quantitative description of biotic and abiotic functions of soil aggregates including diffusion and storage of mass and energy as well as role of aggregates as hot spots of nutrient accumulation, biodiversity, and biogeochemical cycles.

Effects of environmental factors on MSP21-25 aggregation indicate the roles of hydrophobic and electrostatic interactions in the aggregation process.